2GUM | Genus

Total Genus 139

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	139
sequence length	615
structure length	576
Chain Sequence	ANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIHA

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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Time for openFile(/file/5cfd1c0e8199e9cd72c2ac0c/pdb.gz): 1249 ms

reading 576 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

576 atoms created

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

Time for creating model: 61 ms

Adding embedded #jmolscript: select ({0:575});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	Crystal structure of glycoprotein B from herpes simplex virus 1. pubmed doi rcsb
molecule keywords	Glycoprotein B
total genus	139
structure length	576
sequence length	615
chains with identical sequence	B, C
ec nomenclature
pdb deposition date	2006-05-01

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	2gumA03
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	2gumA01

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

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

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

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

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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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2GUMA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations