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


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