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


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