3NW8A

Glycoprotein b from herpes simplex virus type 1, y179s mutant, high-ph
Total Genus 137
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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
Loading diagram...

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

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

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


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