3NWDA

Glycoprotein b from herpes simplex virus type 1, y179s mutant, low-ph
Total Genus 123
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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
123
sequence length
620
structure length
606
Chain Sequence
IKAENTDANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRSSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYLANGGFLIAYQPLLSNTLAELYVREHLREQSRKPPVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVI
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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 123
structure length 606
sequence length 620
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 3nwdA03
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 3nwdA01
4OSNA 4L1RA 3NWFA 3NW8A 3NWAA 4HSIA 3FVCA 3NWDA 4OT1A 2GUMA
chains in the Genus database with same CATH superfamily
4L1RA 2B5RC 2YSZA 2P0HA 2UVMA 2DA0A 4HB0B 2AEHA 3HSAA 2PXGA 2FJUB 4A6FB 4QJ4B 1OQNA 2GCLA 3SYXA 1GC7A 2K00A 2LKOA 2Z0QA 3G9WA 1FHXA 3KRXA 2DKQA 2YS1A 3KRWA 4F7UP 1H4RA 1UPRA 3B77A 3KY9A 5HE1A 3SUZA 4DIXA 4HDOA 4PNKA 4Z2NA 1E5WA 5LOPB 2IYBA 5JHGA 5D0QE 3BINA 3C4OB 3PEGA 2RVBB 5J3TA 1W1HA 2K8EA 5FI0A 1RJ2A 3NW8A 2MFQA 3X23A 3MPXA 1U27A 3VIAA 3T06A 2I5CA 1PMSA 4ZRIA 3SO6A 1MKEA 1XX0A 2DYQA 5DIFB 4HAZB 1NI2A 1NU2A 3OHMB 5D3XA 2J0KA 1BTKA 5CLLB 4CYEA 1WGUA 3TFMA 1WJ1A 1V61A 3TW1A 4KAXB 2K2JA 1KZ7A 1U5EA 1IRSA 1V89A 2D9ZA 5DI9B 1SGHA 2CY5A 2OQBA 4HDQA 3U12A 2DHJA 1MAIA 1S0WC 2K49A 1V5UA 2YVCA 3HIEA 2K2UA 2NBVA 4NY0A 2YS5A 1FOEA 2NZ8B 2RRFA 3GMUB 3WA0A 3RCPA 4K17A 2QKLA 4Z2MB 2L1CA 3D4EA 1V5PA 1SHCA 1U5GA 1UNPA 1MIZB 4K81A 1K5DB 2DN6A 2D9XA 1XD4A 4QJ5B 1RRPB 3P7ZA 5C16A 4MK0A 5DHAB 2IFSA 1ZSQA 2D10A 2KCJA 4GNKB 2VKIA 1BTNA 4MT7A 5KCVA 1UNQA 3AU4A 2YT2A 3A8QA 4D6WA 2Z0OA 2RLOA 2LG1A 4Y94A 5LG4B 1TJ6A 1OMWA 1V5MA 3FVCA 5LONB 2Z59A 2CRFA 2LOXA 2UZSA 1PFJA 2ELAA 4K2OA 2KM7A 3CXBB 2R09A 4DX8A 3DXDA 4XWXA 3ODWA 3LJUX 3N4IB 1ZC4B 1FB8A 2M14A 4OSNA 2I1JA 2COAA 1KZGA 1PLSA 1TQZA 1XODA 2W2WA 2V76A 1N3HA 3DXEA 4DBBA 4F7GA 2Y8FA 1EF1A 2LOZA 3PP2A 3C4PB 3TCAA 2GJYA 4GPTB 1FHOA 2I5FA 2XQNM 2Z13A 3U8ZA 1M7EA 4WVFB 1ISNA 1U5FA 2CODA 1ZYIA 4EMOA 3E2LC 2DX1A 1OY2A 4EKUA 1NTYA 4KHOA 2Z14A 1DDWA 1FGZA 4YONA 5KQ1A 2Q13A 4HB4B 2LULA 3QWMA 4PQ0A 4C0AA 4HSIA 1KI1B 5AYWE 2EC1A 2YS3A 1B55A 3KSYA 4BBKA 1DDMA 2H7EA 4HB2B 4GN1A 4IFSA 2ELBA 5IRSA 2P8VA 3E2KC 2D11A 2KIGA 1MI1A 1ZM0A 1LB1A 2N23A 4DM5A 3C7VB 1FAOA 4A6KA 4L6EA 2R2YA 4B6HA 2P0FA 2Y7BA 4F7HA 4WSFA 5I2MA 3F0WA 5EFXA 3KZ1A 5DHFB 3A58A 5C6RA 4DX90 2G35A 2JP2A 3PG7A 1JTGB 2ROVA 4MY6A 4CSQA 4D0NB 5CLQB 1Q67A 2D4QA 3TO1A 1GG3A 2NMBA 3AU5A 1NTVA 5C5BA 4HAWB 4GMXB 3SNHA 2DLWA 3ZDTA 2RUKB 2L2IA 3PZDA 2CY4A 5DH9B 2J0MA 4KHBB 1DBHA 4KHBA 1MIXA 2J0JA 3A98B 1WI1A 4A6HA 4GXBA 2KUPA 5D27A 2KXXA 3ZVRA 2KUQA 2G2UB 3PSCA 4QJ3B 2LYDA 4KHAA 2Z4DA 5JHHA 2DHKA 2DYNA 2DHIA 3A8PA 4WJ7A 1J0WA 4K2PA 2W2XC 1V88A 3P6AA 3N7CA 2DX5A 4TYZA 3PVWA 1U5DA 1XCGA 5HE3A 1P6SA 3FM8C 4CHJA 1Y5OA 3NSUA 2YRYA 4HB3B 2YH9A 1M7RA 4OT1A 2OTXA 2KGXB 1K5GB 3C7UB 2CAYA 2D9VA 3BJIA 3CIKA 4GOUA 3M1IB 2H7DA 4HAUB 3ODOA 2UZRA 3D8EA 1X05A 1X1FA 1XXMC 2KR0A 4GZUA 5J3QA 2ROZB 4A6FA 4ZRJA 1LW3A 1XKEA 3UZTA 1UNRA 2DFKA 3U7DA 1EGXA 1I7AA 3FSSA 5JLJB 1J19A 2RNRB 1Z87A 1BWNA 3F5RA 3NWFA 3OANA 3QBVB 2M38A 2GCJA 1GC6A 1QQGA 2VRWB 1Y19B 1EVHA 1UPQA 3ULCA 1I2HA 2DTCA 3HW2B 4H8SA 2EMSA 2BCJA 1U29A 4TKNA 1W1GA 3GYOA 5D3VA 3VOQA 4IOYX 3V5WA 2RSGA 3HQCA 3MDBC 1X1GA 2D9WA 2COCA 5D3YA 2AL6A 1P3RA 1DYNA 5L81A 3TVVA 2GUMA 1QC6A 1U2BA 4HATB 3QIJA 2QKMA 3D8DA 1ZC3B 2Z0PA 2D9YA 2RGNB 5D0OE 3DXCA 3PVUA 3D8FA 2D2QA 2PZ1A 2HE7A 1EAZA 2VSZA 5KQ4A 2FJLA 2KIEA 3ODXA 2ZPYA 5I2SA 1WVHA 4YL8A 5C5BB 3GYPA 2DKPA 1WGQA 2J59M 4A5KA 1UEFA 2MKRA 4HHVA 1MK7B 1X86A 4HAVB 3IVFA 5J3YA 5FI1A 1T77A 5GOWB 3NWDA 1DDVA 3FEHA 3WYFB 4QXAB 1WG7A 1H10A 5JP4A 1XR0B 3PVLA 2I1KA 1AQCA 1WJMA 1BAKA 5HE2A 2YF0A 4KVGB 2MWNB 1W1DA 2YT0A 2R0DA 4ZRKA 2MDXA 1AWEA 4CHMA 2COFA 2G2WB 3HK0A 1TXDA 3NWAA 2X18A 2N0YA 1X11A 2ADZA 4NSWA 3DCXA 2YT1A 4GMVA 5M4YB 4EJNA 5HE0A 5C79A 2GS0A 1MK9B 1MPHA 3ML4A 2HTHB 2Y8GA 3ULBA 2EMTA 2ZKMX 4P7IA 3O96A 3SV1A 1FHWA 2P0DA 4IAPA 5D3WA 2EJ8A 3AJ4A 1P5TA 2E2XA 1DROA 4DXAB 4HAXB 4HAYB 5EKQE 1ZVRA 2W2XD 1FGYA
chains in the Genus database with same CATH topology
4L1RA 3NWFA 2B5RC 2GCJA 1JTGB 5LG4B 2PXGA 2FJUB 3FVCA 4QJ4B 2GCLA 2Z59A 4CSQA 3GYOA 4IOYX 2KM7A 3TO1A 4DIXA 4Z2NA 5D0QE 4KHBB 3C4OB 3N4IB 3TVVA 2GUMA 4KHBA 4OSNA 2K8EA 3NW8A 5D0OE 2KXXA 2KUQA 2G2UB 4QJ3B 2KIEA 4KHAA 2Z4DA 5I2SA 3C4PB 2Z13A 3GYPA 3OHMB 1ZYIA 3E2LC 4KHOA 3TW1A 2Z14A 3NWDA 4QXAB 4PQ0A 2YH9A 3U12A 1S0WC 2K49A 4HSIA 4OT1A 3HIEA 5AYWE 2NBVA 3C7UB 4IFSA 5IRSA 2RRFA 4GOUA 3E2KC 2KIGA 3GMUB 2G2WB 3NWAA 4DM5A 3C7VB 4Z2MB 3D4EA 2R2YA 1XXMC 2KR0A 5M4YB 4QJ5B 2ZKMX 5I2MA 4GNKB 3FSSA 3A58A 2YT2A 4D6WA 5EKQE
chains in the Genus database with same CATH homology


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