3NW8 | Genus

Total Genus 137

The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus	137
sequence length	622
structure length	607
Chain Sequence	DIKAENTDANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRSSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYLANGGFLIAYQPLLSNTLAELYVREHLREQSRKPVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIH

The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

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The Resolver thinks Pdb

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Time for openFile(/file/5cffb9e2c1298f547ea88f49/pdb.gz): 1062 ms

reading 607 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

607 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 61 ms

Adding embedded #jmolscript: select ({0:606});backbone only;select *;

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Viral protein
source organism	Human herpesvirus 1
publication title	Structural basis of local, pH-dependent conformational changes in glycoprotein B from herpes simplex virus type 1. pubmed doi rcsb
molecule keywords	Envelope glycoprotein B
total genus	137
structure length	607
sequence length	622
chains with identical sequence	B, C, D
ec nomenclature
pdb deposition date	2010-07-09

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00606	Glycoprotein_B	Herpesvirus Glycoprotein B ectodomain
A	PF17416	Glycoprot_B_PH1	Herpesvirus Glycoprotein B
A	PF17417	Glycoprot_B_PH2	Herpesvirus Glycoprotein B PH-like domain

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
2.30.29.100	Mainly Beta	Roll	PH-domain like	PH-domain like	3nw8A03
3.30.1450.20	Alpha Beta	2-Layer Sandwich	Beta-lactamase Inhibitory Protein; Chain:B, domain 1	Beta-lactamase Inhibitory Protein; Chain:B, domain 1	3nw8A01

3NWFA 3NWDA 3NW8A 4HSIA 2GUMA 4OT1A 3FVCA 4OSNA 3NWAA 4L1RA
chains in the Genus database with same CATH superfamily

1MKEA 4DBBA 4EJNA 2D11A 4WJ7A 2NBVA 2CRFA 2RNRB 3D8DA 3FEHA 2J0JA 4QJ5B 3N4IB 2KR0A 1P5TA 4HDQA 3F5RA 3G9WA 4D6WA 4MY6A 2QKLA 5C79A 5KQ4A 2G35A 1P3RA 1ISNA 5EKQE 2Z0OA 1FGZA 2DFKA 2B5RC 2D2QA 3O96A 5IRSA 1FOEA 1RRPB 3U8ZA 4HDOA 5D27A 1KZ7A 1W1HA 1X11A 1XD4A 2J59M 3ODXA 1ZC3B 1U29A 1V5MA 3U7DA 2ZPYA 4CSQA 1NU2A 3C7UB 2LOZA 3D8EA 1BTNA 2K2JA 4BBKA 4GMXB 4GMVA 4HAWB 2PZ1A 1WGUA 2XQNM 2ADZA 2COFA 3A8PA 1ZC4B 3F0WA 1XX0A 2EMSA 2Z59A 2UZSA 4C0AA 1JTGB 1FAOA 3PVLA 2E2XA 4YONA 4KVGB 1V89A 3M1IB 1XR0B 3NW8A 3PEGA 2Z14A 5DHFB 5DIFB 2DKQA 4Z2MB 3VOQA 1U5EA 4NY0A 4MK0A 2D9WA 4D0NB 1WVHA 2D9VA 2DTCA 2P0DA 2D9XA 2JP2A 5JHHA 1X86A 3P7ZA 5D0QE 4GNKB 1OQNA 3RCPA 1U5DA 1X1GA 1I7AA 2RVBB 3NWDA 4HSIA 3FVCA 2YRYA 5I2MA 5M4YB 3PSCA 4EKUA 1NTYA 1OMWA 4K81A 1GG3A 2KUPA 2YT2A 3X23A 3QIJA 2W2XC 1ZSQA 2MKRA 4HAZB 3DXDA 2GCLA 1EGXA 1GC7A 2IYBA 2LKOA 4PNKA 5HE0A 2LULA 3FM8C 3D4EA 2EJ8A 3LJUX 3AJ4A 2QKMA 2L2IA 2K8EA 3TVVA 5HE1A 1Q67A 1M7RA 3SUZA 1SGHA 5J3QA 4GN1A 3C4OB 1PFJA 3OANA 4B6HA 1V5UA 5C16A 4OT1A 4ZRKA 2CODA 4DX8A 1K5GB 2GUMA 2D10A 1K5DB 5C5BA 2K00A 4HB3B 5JHGA 1FGYA 5D3XA 5AYWE 1QQGA 5GOWB 3KY9A 4IFSA 3VIAA 2DA0A 1LB1A 2YT0A 3NSUA 2LYDA 5C5BB 2COCA 1U27A 2FJLA 1KI1B 3SO6A 4L6EA 2YF0A 4KHBA 2W2XD 3QBVB 4QJ3B 2P0HA 5LG4B 1U2BA 2DKPA 2D4QA 2UZRA 1UNPA 2I5FA 1ZYIA 4KHBB 4MT7A 5DH9B 1MAIA 1X1FA 1NI2A 1FHWA 2OQBA 4DX90 3AU5A 5D3WA 5JLJB 2Y7BA 1T77A 3SYXA 3HQCA 5J3TA 1J0WA 3DXCA 3PVUA 4QXAB 3ODOA 4DXAB 2DHIA 4H8SA 4IOYX 3BJIA 1PLSA 1MIXA 2DN6A 5HE3A 2MWNB 5I2SA 2M14A 4A6KA 1DDVA 3PG7A 4F7HA 1FB8A 1H4RA 1UPRA 3DCXA 1UPQA 2EMTA 2YS3A 4KHOA 4Y94A 4DM5A 1H10A 5D3YA 3NWFA 3ZDTA 1DYNA 2YS1A 2Z13A 1EAZA 1WGQA 2RUKB 3N7CA 5KCVA 4DIXA 2COAA 2MFQA 5J3YA 2MDXA 3OHMB 4HB2B 4GPTB 3E2KC 4CHJA 2IFSA 3D8FA 2ROVA 2D9ZA 2CAYA 3E2LC 1KZGA 1V88A 2ELAA 2NMBA 5CLLB 3B77A 2LOXA 5HE2A 1U5GA 2PXGA 1V5PA 2GJYA 2W2WA 3TFMA 4IAPA 2KXXA 3T06A 3A58A 4A6HA 1XXMC 1X05A 3WYFB 2Y8GA 1BTKA 2AEHA 2Y8FA 3KRWA 1OY2A 4HAVB 3CIKA 5EFXA 2ROZB 3NWAA 1GC6A 4Z2NA 1UEFA 4KHAA 1TXDA 2K49A 1AQCA 1DDWA 1P6SA 5DHAB 4YL8A 1BWNA 3V5WA 4CYEA 2KGXB 2KUQA 4KAXB 3ULCA 1PMSA 4QJ4B 1UNQA 1WI1A 4F7GA 3KSYA 1MK7B 2KIEA 1WG7A 3U12A 1B55A 1MIZB 2YVCA 2Z0QA 2YH9A 1DBHA 1J19A 2AL6A 2DLWA 2ZKMX 3HSAA 4K17A 1XODA 2I1KA 2I5CA 4NSWA 2GS0A 3A98B 4GOUA 4CHMA 3HIEA 1U5FA 4L1RA 2Z0PA 3IVFA 2DX5A 4HAXB 5LONB 2J0KA 2ELBA 3TO1A 1WJMA 4GXBA 4TKNA 3QWMA 5D0OE 4HB0B 3GMUB 2VSZA 1W1GA 4OSNA 3P6AA 3HK0A 3PVWA 2KM7A 4PQ0A 5JP4A 1Z87A 4EMOA 2YT1A 3A8QA 2K2UA 2M38A 1MI1A 2CY4A 4HAUB 3TCAA 2DYQA 2R2YA 2X18A 1XCGA 3SV1A 1ZVRA 3C4PB 2GCJA 2VRWB 1S0WC 2EC1A 1SHCA 2N23A 2P8VA 1EVHA 2Q13A 2KCJA 4GZUA 4A5KA 1Y19B 4ZRJA 3CXBB 1ZM0A 1FHXA 2OTXA 3BINA 2N0YA 1Y5OA 2FJUB 4WVFB 2DHKA 1EF1A 2L1CA 1E5WA 1V61A 3GYOA 2VKIA 2RSGA 1IRSA 4WSFA 1QC6A 2NZ8B 3PP2A 3SNHA 2G2WB 3HW2B 1W1DA 3KRXA 2D9YA 1DDMA 4HHVA 2RLOA 2CY5A 4HAYB 2HTHB 2Z4DA 4A6FA 1MPHA 2HE7A 5FI1A 4K2PA 3MDBC 2DHJA 1AWEA 2UVMA 1WJ1A 4F7UP 4A6FB 2KIGA 2RGNB 2DYNA 4ZRIA 4TYZA 3UZTA 2H7DA 3AU4A 3MPXA 4P7IA 2R0DA 3GYPA 3WA0A 1NTVA 2G2UB 3ODWA 5CLQB 5DI9B 2P0FA 1UNRA 4HATB 2LG1A 3PZDA 1TJ6A 3DXEA 3C7VB 2R09A 1FHOA 2I1JA 3KZ1A 1LW3A 1XKEA 1DROA 1I2HA 3ULBA 1RJ2A 3ZVRA 2YSZA 5C6RA 4XWXA 5KQ1A 1M7EA 2BCJA 2DX1A 1TQZA 4K2OA 3TW1A 1BAKA 2RRFA 1N3HA 1MK9B 5D3VA 2V76A 4HB4B 5LOPB 3ML4A 5FI0A 2YS5A 2J0MA 5L81A 2H7EA 3FSSA
chains in the Genus database with same CATH topology

4PQ0A 4KHOA 4DM5A 2NBVA 4QJ5B 3N4IB 3NWFA 2KR0A 2GCLA 2Z13A 2R2YA 4D6WA 3FSSA 3C4PB 4DIXA 2GCJA 5EKQE 3D4EA 1S0WC 3OHMB 2K8EA 2B5RC 3E2KC 3TVVA 3E2LC 5IRSA 3C4OB 2FJUB 2PXGA 4OT1A 2KXXA 3GYOA 3A58A 1XXMC 4CSQA 2GUMA 3C7UB 2G2WB 5AYWE 4IFSA 3NWAA 2Z4DA 4Z2NA 4KHAA 2Z59A 2K49A 1JTGB 2KUQA 2KIGA 4QJ4B 4KHBA 2G2UB 3GYPA 3NW8A 2KIEA 4QJ3B 3U12A 5LG4B 2Z14A 2YH9A 1ZYIA 4Z2MB 4KHBB 2ZKMX 3C7VB 4GOUA 4QXAB 5D0QE 4GNKB 3HIEA 4L1RA 3TW1A 3NWDA 2RRFA 4IOYX 4HSIA 3FVCA 3TO1A 5I2MA 5M4YB 5D0OE 5I2SA 3GMUB 2YT2A 4OSNA 2KM7A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3NWF A;  3NWD A;  3NW8 A;  4HSI A;  2GUM A;  4OT1 A;  3FVC A;  4OSN A;  3NWA A;  4L1R A; 
#chains in the Genus database with same CATH topology
 1MKE A;  4DBB A;  4EJN A;  2D11 A;  4WJ7 A;  2NBV A;  2CRF A;  2RNR B;  3D8D A;  3FEH A;  2J0J A;  4QJ5 B;  3N4I B;  2KR0 A;  1P5T A;  4HDQ A;  3F5R A;  3G9W A;  4D6W A;  4MY6 A;  2QKL A;  5C79 A;  5KQ4 A;  2G35 A;  1P3R A;  1ISN A;  5EKQ E;  2Z0O A;  1FGZ A;  2DFK A;  2B5R C;  2D2Q A;  3O96 A;  5IRS A;  1FOE A;  1RRP B;  3U8Z A;  4HDO A;  5D27 A;  1KZ7 A;  1W1H A;  1X11 A;  1XD4 A;  2J59 M;  3ODX A;  1ZC3 B;  1U29 A;  1V5M A;  3U7D A;  2ZPY A;  4CSQ A;  1NU2 A;  3C7U B;  2LOZ A;  3D8E A;  1BTN A;  2K2J A;  4BBK A;  4GMX B;  4GMV A;  4HAW B;  2PZ1 A;  1WGU A;  2XQN M;  2ADZ A;  2COF A;  3A8P A;  1ZC4 B;  3F0W A;  1XX0 A;  2EMS A;  2Z59 A;  2UZS A;  4C0A A;  1JTG B;  1FAO A;  3PVL A;  2E2X A;  4YON A;  4KVG B;  1V89 A;  3M1I B;  1XR0 B;  3NW8 A;  3PEG A;  2Z14 A;  5DHF B;  5DIF B;  2DKQ A;  4Z2M B;  3VOQ A;  1U5E A;  4NY0 A;  4MK0 A;  2D9W A;  4D0N B;  1WVH A;  2D9V A;  2DTC A;  2P0D A;  2D9X A;  2JP2 A;  5JHH A;  1X86 A;  3P7Z A;  5D0Q E;  4GNK B;  1OQN A;  3RCP A;  1U5D A;  1X1G A;  1I7A A;  2RVB B;  3NWD A;  4HSI A;  3FVC A;  2YRY A;  5I2M A;  5M4Y B;  3PSC A;  4EKU A;  1NTY A;  1OMW A;  4K81 A;  1GG3 A;  2KUP A;  2YT2 A;  3X23 A;  3QIJ A;  2W2X C;  1ZSQ A;  2MKR A;  4HAZ B;  3DXD A;  2GCL A;  1EGX A;  1GC7 A;  2IYB A;  2LKO A;  4PNK A;  5HE0 A;  2LUL A;  3FM8 C;  3D4E A;  2EJ8 A;  3LJU X;  3AJ4 A;  2QKM A;  2L2I A;  2K8E A;  3TVV A;  5HE1 A;  1Q67 A;  1M7R A;  3SUZ A;  1SGH A;  5J3Q A;  4GN1 A;  3C4O B;  1PFJ A;  3OAN A;  4B6H A;  1V5U A;  5C16 A;  4OT1 A;  4ZRK A;  2COD A;  4DX8 A;  1K5G B;  2GUM A;  2D10 A;  1K5D B;  5C5B A;  2K00 A;  4HB3 B;  5JHG A;  1FGY A;  5D3X A;  5AYW E;  1QQG A;  5GOW B;  3KY9 A;  4IFS A;  3VIA A;  2DA0 A;  1LB1 A;  2YT0 A;  3NSU A;  2LYD A;  5C5B B;  2COC A;  1U27 A;  2FJL A;  1KI1 B;  3SO6 A;  4L6E A;  2YF0 A;  4KHB A;  2W2X D;  3QBV B;  4QJ3 B;  2P0H A;  5LG4 B;  1U2B A;  2DKP A;  2D4Q A;  2UZR A;  1UNP A;  2I5F A;  1ZYI A;  4KHB B;  4MT7 A;  5DH9 B;  1MAI A;  1X1F A;  1NI2 A;  1FHW A;  2OQB A;  4DX9 0;  3AU5 A;  5D3W A;  5JLJ B;  2Y7B A;  1T77 A;  3SYX A;  3HQC A;  5J3T A;  1J0W A;  3DXC A;  3PVU A;  4QXA B;  3ODO A;  4DXA B;  2DHI A;  4H8S A;  4IOY X;  3BJI A;  1PLS A;  1MIX A;  2DN6 A;  5HE3 A;  2MWN B;  5I2S A;  2M14 A;  4A6K A;  1DDV A;  3PG7 A;  4F7H A;  1FB8 A;  1H4R A;  1UPR A;  3DCX A;  1UPQ A;  2EMT A;  2YS3 A;  4KHO A;  4Y94 A;  4DM5 A;  1H10 A;  5D3Y A;  3NWF A;  3ZDT A;  1DYN A;  2YS1 A;  2Z13 A;  1EAZ A;  1WGQ A;  2RUK B;  3N7C A;  5KCV A;  4DIX A;  2COA A;  2MFQ A;  5J3Y A;  2MDX A;  3OHM B;  4HB2 B;  4GPT B;  3E2K C;  4CHJ A;  2IFS A;  3D8F A;  2ROV A;  2D9Z A;  2CAY A;  3E2L C;  1KZG A;  1V88 A;  2ELA A;  2NMB A;  5CLL B;  3B77 A;  2LOX A;  5HE2 A;  1U5G A;  2PXG A;  1V5P A;  2GJY A;  2W2W A;  3TFM A;  4IAP A;  2KXX A;  3T06 A;  3A58 A;  4A6H A;  1XXM C;  1X05 A;  3WYF B;  2Y8G A;  1BTK A;  2AEH A;  2Y8F A;  3KRW A;  1OY2 A;  4HAV B;  3CIK A;  5EFX A;  2ROZ B;  3NWA A;  1GC6 A;  4Z2N A;  1UEF A;  4KHA A;  1TXD A;  2K49 A;  1AQC A;  1DDW A;  1P6S A;  5DHA B;  4YL8 A;  1BWN A;  3V5W A;  4CYE A;  2KGX B;  2KUQ A;  4KAX B;  3ULC A;  1PMS A;  4QJ4 B;  1UNQ A;  1WI1 A;  4F7G A;  3KSY A;  1MK7 B;  2KIE A;  1WG7 A;  3U12 A;  1B55 A;  1MIZ B;  2YVC A;  2Z0Q A;  2YH9 A;  1DBH A;  1J19 A;  2AL6 A;  2DLW A;  2ZKM X;  3HSA A;  4K17 A;  1XOD A;  2I1K A;  2I5C A;  4NSW A;  2GS0 A;  3A98 B;  4GOU A;  4CHM A;  3HIE A;  1U5F A;  4L1R A;  2Z0P A;  3IVF A;  2DX5 A;  4HAX B;  5LON B;  2J0K A;  2ELB A;  3TO1 A;  1WJM A;  4GXB A;  4TKN A;  3QWM A;  5D0O E;  4HB0 B;  3GMU B;  2VSZ A;  1W1G A;  4OSN A;  3P6A A;  3HK0 A;  3PVW A;  2KM7 A;  4PQ0 A;  5JP4 A;  1Z87 A;  4EMO A;  2YT1 A;  3A8Q A;  2K2U A;  2M38 A;  1MI1 A;  2CY4 A;  4HAU B;  3TCA A;  2DYQ A;  2R2Y A;  2X18 A;  1XCG A;  3SV1 A;  1ZVR A;  3C4P B;  2GCJ A;  2VRW B;  1S0W C;  2EC1 A;  1SHC A;  2N23 A;  2P8V A;  1EVH A;  2Q13 A;  2KCJ A;  4GZU A;  4A5K A;  1Y19 B;  4ZRJ A;  3CXB B;  1ZM0 A;  1FHX A;  2OTX A;  3BIN A;  2N0Y A;  1Y5O A;  2FJU B;  4WVF B;  2DHK A;  1EF1 A;  2L1C A;  1E5W A;  1V61 A;  3GYO A;  2VKI A;  2RSG A;  1IRS A;  4WSF A;  1QC6 A;  2NZ8 B;  3PP2 A;  3SNH A;  2G2W B;  3HW2 B;  1W1D A;  3KRX A;  2D9Y A;  1DDM A;  4HHV A;  2RLO A;  2CY5 A;  4HAY B;  2HTH B;  2Z4D A;  4A6F A;  1MPH A;  2HE7 A;  5FI1 A;  4K2P A;  3MDB C;  2DHJ A;  1AWE A;  2UVM A;  1WJ1 A;  4F7U P;  4A6F B;  2KIG A;  2RGN B;  2DYN A;  4ZRI A;  4TYZ A;  3UZT A;  2H7D A;  3AU4 A;  3MPX A;  4P7I A;  2R0D A;  3GYP A;  3WA0 A;  1NTV A;  2G2U B;  3ODW A;  5CLQ B;  5DI9 B;  2P0F A;  1UNR A;  4HAT B;  2LG1 A;  3PZD A;  1TJ6 A;  3DXE A;  3C7V B;  2R09 A;  1FHO A;  2I1J A;  3KZ1 A;  1LW3 A;  1XKE A;  1DRO A;  1I2H A;  3ULB A;  1RJ2 A;  3ZVR A;  2YSZ A;  5C6R A;  4XWX A;  5KQ1 A;  1M7E A;  2BCJ A;  2DX1 A;  1TQZ A;  4K2O A;  3TW1 A;  1BAK A;  2RRF A;  1N3H A;  1MK9 B;  5D3V A;  2V76 A;  4HB4 B;  5LOP B;  3ML4 A;  5FI0 A;  2YS5 A;  2J0M A;  5L81 A;  2H7E A;  3FSS A; 
#chains in the Genus database with same CATH homology
 4PQ0 A;  4KHO A;  4DM5 A;  2NBV A;  4QJ5 B;  3N4I B;  3NWF A;  2KR0 A;  2GCL A;  2Z13 A;  2R2Y A;  4D6W A;  3FSS A;  3C4P B;  4DIX A;  2GCJ A;  5EKQ E;  3D4E A;  1S0W C;  3OHM B;  2K8E A;  2B5R C;  3E2K C;  3TVV A;  3E2L C;  5IRS A;  3C4O B;  2FJU B;  2PXG A;  4OT1 A;  2KXX A;  3GYO A;  3A58 A;  1XXM C;  4CSQ A;  2GUM A;  3C7U B;  2G2W B;  5AYW E;  4IFS A;  3NWA A;  2Z4D A;  4Z2N A;  4KHA A;  2Z59 A;  2K49 A;  1JTG B;  2KUQ A;  2KIG A;  4QJ4 B;  4KHB A;  2G2U B;  3GYP A;  3NW8 A;  2KIE A;  4QJ3 B;  3U12 A;  5LG4 B;  2Z14 A;  2YH9 A;  1ZYI A;  4Z2M B;  4KHB B;  2ZKM X;  3C7V B;  4GOU A;  4QXA B;  5D0Q E;  4GNK B;  3HIE A;  4L1R A;  3TW1 A;  3NWD A;  2RRF A;  4IOY X;  4HSI A;  3FVC A;  3TO1 A;  5I2M A;  5M4Y B;  5D0O E;  5I2S A;  3GMU B;  2YT2 A;  4OSN A;  2KM7 A;

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similar chains in the Genus database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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3NW8A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations