3NWFA

Glycoprotein b from herpes simplex virus type 1, low-ph
Total Genus 142
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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
142
sequence length
622
structure length
605
Chain Sequence
DIKAENTDANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYLANGGFLIAYQPLLSNTLAELYVREHLREQSRKPVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIH
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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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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
molecule keywords Envelope glycoprotein B
total genus 142
structure length 605
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 3nwfA03
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 3nwfA01
3NWAA 3NWDA 4OT1A 4HSIA 2GUMA 3FVCA 3NWFA 4OSNA 3NW8A 4L1RA
chains in the Genus database with same CATH superfamily
2D9WA 5KQ4A 3TVVA 1Y19B 5HE0A 2NZ8B 1GC6A 1BAKA 4HAWB 1I2HA 2YH9A 1Y5OA 1FHXA 2GJYA 4C0AA 1W1HA 4ZRIA 3SUZA 1LB1A 5LG4B 3G9WA 5CLQB 2GUMA 3ULBA 1V61A 3TW1A 2DHIA 1H4RA 5J3YA 1UPRA 3DXEA 3SYXA 2K00A 1FOEA 1DYNA 4NY0A 3NWFA 2VSZA 4HAXB 4KHAA 2RLOA 2GCJA 4QJ4B 3E2KC 2I5FA 4EMOA 4DM5A 2IYBA 2LG1A 1ZC4B 2YSZA 3KZ1A 4GOUA 1DDMA 1TJ6A 4KAXB 4GMXB 2YT1A 2RUKB 1X11A 3T06A 2KIGA 3UZTA 3IVFA 1WGUA 4Y94A 1EF1A 3NW8A 4H8SA 2CAYA 2LOXA 2J0MA 2UZSA 3WA0A 3D8DA 2DN6A 2L1CA 2N0YA 2DFKA 3D8EA 3NWAA 1OQNA 5AYWE 3VOQA 1J19A 2LULA 4BBKA 5C5BB 1MK9B 2HE7A 1NTVA 3BJIA 1WJMA 5D3WA 1QC6A 4A6KA 3C4OB 1XODA 4MT7A 5JP4A 2M14A 1U5DA 1DROA 2ROVA 1WGQA 3AU5A 2QKMA 4L1RA 3HQCA 1P6SA 3HIEA 4CHJA 2P0DA 4OT1A 3WYFB 4MK0A 2KXXA 4F7HA 4HB4B 4CHMA 1QQGA 2YVCA 3ODXA 3V5WA 1V89A 1T77A 3KRWA 4KHBB 4WVFB 3GMUB 1ISNA 2E2XA 3PSCA 3A58A 1TXDA 4HAZB 3SO6A 3TO1A 2AEHA 5J3QA 3QBVB 3ZVRA 1X86A 2COCA 4DBBA 4WSFA 2L2IA 2P8VA 4HB3B 4TKNA 1UNPA 3B77A 3HW2B 2Z0QA 2R09A 2COFA 2KCJA 1MIZB 4PQ0A 1BTKA 1Q67A 3FEHA 1J0WA 2RVBB 1EGXA 4HDQA 1AQCA 2V76A 1X1FA 1WVHA 2D4QA 1FHWA 4GPTB 2MDXA 5DIFB 2J0KA 2EJ8A 3D4EA 4A5KA 1EAZA 2YRYA 2W2WA 2FJUB 2I1KA 3U12A 3ODWA 2DKPA 2RNRB 2OTXA 2H7EA 4Z2MB 3TFMA 4A6FA 3C4PB 2HTHB 1I7AA 3KY9A 3M1IB 5M4YB 2XQNM 3OANA 1UPQA 1ZC3B 3MDBC 1MKEA 1UEFA 3NWDA 2DHKA 4DIXA 3FSSA 1PLSA 5KCVA 2FJLA 1W1DA 4GNKB 5HE1A 3KRXA 2LYDA 1V5PA 2Y8FA 2MWNB 4ZRJA 2EMTA 4GMVA 2G2UB 3DXCA 1V88A 1U5GA 1AWEA 1PFJA 1U27A 1XCGA 3ULCA 1BTNA 5DI9B 5HE2A 3A8PA 1TQZA 2GS0A 2D9VA 3CIKA 2DLWA 1P3RA 2RSGA 1H10A 2J0JA 2QKLA 3U7DA 2H7DA 2YT0A 1XR0B 1NTYA 4Z2NA 2DYNA 1NU2A 2JP2A 5JHGA 2RGNB 1M7EA 3P6AA 4QXAB 4IFSA 3D8FA 1UNQA 3A98B 4IAPA 1ZVRA 2Y8GA 2D9ZA 4KHBA 4A6HA 2COAA 1S0WC 2D11A 3ZDTA 1WG7A 2OQBA 5EFXA 4GN1A 3AJ4A 4DX90 4F7GA 2Q13A 2D2QA 3N7CA 1DDWA 2W2XC 4K2OA 1XX0A 2DTCA 2CODA 2MKRA 2K2UA 4KVGB 2IFSA 3CXBB 4HSIA 2R2YA 3VIAA 5D0QE 1MI1A 3A8QA 5L81A 1XXMC 1NI2A 1K5GB 4YONA 4HATB 5I2MA 2LKOA 4DX8A 5DHFB 2DYQA 4B6HA 2G2WB 3LJUX 1SHCA 2ZKMX 2YF0A 2YS3A 2Z59A 2J59M 2Z0PA 3PVLA 2ZPYA 5C5BA 3PZDA 4K2PA 4A6FB 4HHVA 1FB8A 2EMSA 4DXAB 2D9XA 2VRWB 3PP2A 1K5DB 2P0HA 3HK0A 1Z87A 2KIEA 2Z4DA 2UZRA 3X23A 2CY4A 2KUQA 3SV1A 1JTGB 2D9YA 2DX1A 3ML4A 5D27A 3RCPA 1RJ2A 2DHJA 1W1GA 3SNHA 2KR0A 1XD4A 2ADZA 2ELAA 1KZGA 3PVUA 1OY2A 4HB2B 3C7VB 2Z13A 4CYEA 2CRFA 2B5RC 4D6WA 4HAYB 2Z14A 5FI0A 3AU4A 4EJNA 4K17A 4NSWA 1WJ1A 5DHAB 1GC7A 2DA0A 3OHMB 1MK7B 3NSUA 3DCXA 1DBHA 3N4IB 2P0FA 1OMWA 5LOPB 2YT2A 2Y7BA 4YL8A 2YS1A 1IRSA 2EC1A 3DXDA 5D3VA 2I5CA 4OSNA 4L6EA 4ZRKA 3MPXA 2K49A 1KI1B 3GYOA 1RRPB 1U5EA 3F5RA 4XWXA 2NMBA 1ZM0A 1X1GA 5D3XA 1PMSA 1FGYA 4P7IA 2UVMA 1FHOA 2R0DA 1P5TA 5HE3A 5IRSA 2KM7A 1ZSQA 4IOYX 1FAOA 5C6RA 1U2BA 2GCLA 1V5UA 2RRFA 4D0NB 4GZUA 5DH9B 1XKEA 4HB0B 3PG7A 1E5WA 5I2SA 1U29A 1X05A 3P7ZA 3HSAA 2DX5A 2LOZA 5GOWB 2W2XD 1M7RA 1UNRA 3U8ZA 2KUPA 1EVHA 2CY5A 2AL6A 5C16A 1KZ7A 3FM8C 5D0OE 1MIXA 1WI1A 4MY6A 4HAVB 3KSYA 2ROZB 2G35A 2BCJA 5JHHA 5FI1A 5LONB 4GXBA 3PVWA 3BINA 2ELBA 3F0WA 2MFQA 2KGXB 1U5FA 5J3TA 4F7UP 1ZYIA 4PNKA 3FVCA 2PXGA 4HDOA 2Z0OA 3O96A 5JLJB 1B55A 5CLLB 1GG3A 1LW3A 2YS5A 3ODOA 4TYZA 3GYPA 4WJ7A 2M38A 1N3HA 5EKQE 4QJ3B 2DKQA 2N23A 1MPHA 5C79A 4EKUA 1V5MA 4CSQA 3QIJA 2PZ1A 1SGHA 2K2JA 5KQ1A 1FGZA 3QWMA 2K8EA 2VKIA 2X18A 4KHOA 5D3YA 3C7UB 4K81A 1BWNA 2D10A 3PEGA 2NBVA 4HAUB 1DDVA 2I1JA 1MAIA 3E2LC 3TCAA 4QJ5B
chains in the Genus database with same CATH topology
3TVVA 4KHBA 1S0WC 4OSNA 2YH9A 2K49A 3GYOA 4PQ0A 5LG4B 2GUMA 3TW1A 4HSIA 2R2YA 3NWFA 5D0QE 2KM7A 5IRSA 4KHAA 4IOYX 3D4EA 2GCLA 2RRFA 2GCJA 4QJ4B 1XXMC 3E2KC 2FJUB 4DM5A 3U12A 5I2SA 5I2MA 4Z2MB 2G2WB 3C4PB 4GOUA 5M4YB 2KIGA 3NWDA 5D0OE 2ZKMX 4DIXA 2Z59A 3FSSA 3NW8A 4GNKB 3NWAA 5AYWE 2KIEA 2Z4DA 1ZYIA 2KUQA 1JTGB 2G2UB 3FVCA 2PXGA 3C4OB 3GYPA 2KR0A 4L1RA 3HIEA 3C7VB 4OT1A 2Z13A 5EKQE 4QJ3B 2B5RC 4D6WA 2KXXA 2Z14A 4CSQA 4Z2NA 3GMUB 4KHBB 2K8EA 4KHOA 3C7UB 3A58A 3TO1A 3OHMB 2NBVA 4QXAB 4IFSA 3N4IB 3E2LC 4QJ5B 2YT2A
chains in the Genus database with same CATH homology


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