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


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