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


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