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


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