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


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