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


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