2GUMA

Crystal structure of the extracellular domain of glycoprotein b from herpes simplex virus type i
Total Genus 139
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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
139
sequence length
615
structure length
576
Chain Sequence
ANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIHA
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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 Glycoprotein B
publication title Crystal structure of glycoprotein B from herpes simplex virus 1.
pubmed doi rcsb
source organism Human herpesvirus 1
molecule tags Viral protein
total genus 139
structure length 576
sequence length 615
chains with identical sequence B, C
ec nomenclature
pdb deposition date 2006-05-01

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 2gumA03
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 2gumA01
2GUMA 3NWAA 3NWDA 4HSIA 3NWFA 3FVCA 4OT1A 4OSNA 3NW8A 4L1RA
chains in the Genus database with same CATH superfamily
4QJ4B 3PVUA 3OANA 1FHXA 3D4EA 1PLSA 2I1JA 2J0JA 3D8EA 3FVCA 4OSNA 4MK0A 2H7EA 1P3RA 1RJ2A 1MPHA 1EAZA 1P5TA 3PG7A 1AWEA 2P0HA 2LOXA 1X1FA 1PMSA 2ROZB 1W1HA 1W1DA 1XR0B 2G35A 1V88A 3M1IB 1FHOA 2G2UB 5DHAB 3TVVA 3GYPA 1BTKA 2DYNA 1AQCA 1XD4A 2R0DA 3E2LC 4A6FB 2X18A 4NY0A 1XCGA 3PZDA 4PQ0A 1T77A 3P6AA 4KHAA 4HDOA 2M38A 1WGUA 3U12A 2G2WB 1WVHA 2J0KA 4GMVA 3SYXA 1MI1A 3PP2A 1H4RA 5FI0A 1BWNA 4A6KA 1X11A 4CHJA 5KCVA 2DHJA 2RGNB 3UZTA 3C7VB 3N4IB 1MAIA 3PSCA 5JHGA 3GMUB 2RSGA 3OHMB 2MKRA 4D0NB 2DX5A 3KRWA 1I2HA 1MK7B 2DFKA 1KI1B 1FGZA 1GG3A 2CY5A 4HAZB 1FGYA 2YF0A 4HSIA 1V89A 2R2YA 2Y8GA 2Z4DA 3SNHA 4NSWA 2KGXB 2HTHB 3HK0A 4BBKA 2D9WA 4DXAB 1ZSQA 1Y5OA 1W1GA 4QXAB 3AJ4A 1ZVRA 2YS5A 5M4YB 2ROVA 4HDQA 3ULBA 2I5CA 5C16A 1DROA 2VSZA 3ULCA 5D0OE 3P7ZA 1UEFA 2CAYA 2NZ8B 4KAXB 2DYQA 2LYDA 1J0WA 3FM8C 1MK9B 2YRYA 4ZRJA 1H10A 3TFMA 3D8DA 4HATB 3C4PB 2K2JA 5GOWB 3RCPA 4CYEA 4D6WA 4Y94A 1X1GA 2KCJA 1ZC4B 2DX1A 2DTCA 5I2SA 2LG1A 2Z59A 5JHHA 2B5RC 5D0QE 1NI2A 2MFQA 3WYFB 4YL8A 4PNKA 1DYNA 1U2BA 1DDMA 2ELBA 1NTYA 2GCJA 3MDBC 3BINA 1GC7A 2ZPYA 2I1KA 2KUPA 5C5BB 1WJ1A 4KHBB 3KRXA 4DX90 1MKEA 1U5GA 2NMBA 2M14A 1U5FA 3DXEA 2ADZA 4H8SA 3SO6A 3N7CA 2YT2A 4OT1A 4A6HA 1XX0A 3C4OB 1U5DA 3FEHA 1P6SA 2DKQA 4K2PA 2EC1A 1XODA 4HB4B 3E2KC 2P0DA 1J19A 4GNKB 4KVGB 1UPQA 1X86A 3VOQA 5DI9B 1EVHA 5CLQB 5KQ1A 2GJYA 4GN1A 4EMOA 4QJ5B 5C6RA 4EJNA 2H7DA 1U27A 4DBBA 2VRWB 2YVCA 5IRSA 3KY9A 1FOEA 2RRFA 2Z0QA 2EMSA 2KR0A 2MWNB 5D3YA 1SHCA 4CHMA 3CIKA 2UZSA 1DBHA 1K5GB 1JTGB 5EKQE 4WSFA 1NU2A 2BCJA 4CSQA 5FI1A 2Y7BA 3PVLA 4IAPA 4HAWB 3A98B 2HE7A 5C79A 3O96A 5CLLB 1RRPB 1WI1A 2K2UA 2E2XA 2D2QA 4K2OA 3NWFA 1TXDA 3NSUA 2RVBB 4Z2NA 2Z0PA 4DM5A 1WG7A 1SGHA 2DLWA 3NWDA 1V5UA 3D8FA 3U7DA 2P0FA 2NBVA 4HAYB 2W2XC 2AEHA 2YT0A 2N0YA 3ZVRA 3ODXA 5LONB 1DDVA 4GPTB 2PXGA 2GS0A 5D3WA 1UNPA 5J3TA 3SV1A 2K00A 3T06A 4C0AA 3DCXA 2L2IA 4ZRKA 5DH9B 2MDXA 1FB8A 2GCLA 2D11A 2Z13A 2QKLA 3C7UB 4HB2B 2IFSA 2AL6A 2JP2A 3ODOA 3U8ZA 5LOPB 3FSSA 3ODWA 5HE1A 2OQBA 2YH9A 1X05A 4HAXB 3KZ1A 3QBVB 1M7EA 4L6EA 2ELAA 2CRFA 4XWXA 1FAOA 5D3VA 3DXCA 3A58A 2VKIA 1TJ6A 4EKUA 2UZRA 2J0MA 2CY4A 3VIAA 3BJIA 2L1CA 2Z14A 3PVWA 1NTVA 4TYZA 2QKMA 1B55A 4K81A 5D27A 5DHFB 4A6FA 4P7IA 2RUKB 5KQ4A 5AYWE 4GOUA 4Z2MB 4IFSA 1OQNA 3QWMA 5JP4A 5HE3A 5J3YA 2COFA 1GC6A 1LW3A 3LJUX 3HIEA 1QQGA 2D9XA 2RLOA 4L1RA 2D4QA 3DXDA 4WVFB 2PZ1A 2N23A 2YS1A 4WJ7A 3B77A 2D9ZA 4HAUB 5L81A 3CXBB 1K5DB 2COAA 2XQNM 4ZRIA 2LOZA 1BAKA 2Z0OA 2DKPA 3NW8A 1ZYIA 2IYBA 1Y19B 2DN6A 2KIGA 1MIXA 5HE0A 4HHVA 1KZ7A 2KIEA 4MT7A 2D10A 3TO1A 4DX8A 4K17A 3QIJA 2DHKA 2KM7A 1M7RA 3ML4A 4TKNA 3KSYA 1Q67A 2Q13A 1E5WA 2CODA 2FJLA 3F5RA 2D9VA 5DIFB 3G9WA 3HW2B 4GMXB 4GXBA 1TQZA 3MPXA 1WGQA 1PFJA 2OTXA 5EFXA 2GUMA 3NWAA 1XXMC 2D9YA 1UNRA 1OMWA 2I5FA 4F7HA 1QC6A 5D3XA 2K8EA 5I2MA 5C5BA 2COCA 4KHBA 4F7UP 4IOYX 4KHOA 1U29A 2UVMA 2V76A 4QJ3B 3IVFA 2LKOA 2KXXA 1EF1A 3A8PA 2EMTA 1V5PA 1LB1A 2R09A 1S0WC 3HQCA 1EGXA 5HE2A 4A5KA 2W2WA 4HAVB 1UPRA 1Z87A 2YT1A 3PEGA 4HB3B 2EJ8A 3F0WA 2DHIA 2K49A 1IRSA 1XKEA 2FJUB 2P8VA 4F7GA 1DDWA 3TCAA 2W2XD 5J3QA 3X23A 3ZDTA 2J59M 1V61A 1ISNA 3HSAA 4HB0B 1V5MA 2KUQA 2Y8FA 2ZKMX 3TW1A 1I7AA 2LULA 1KZGA 3AU4A 1N3HA 1WJMA 4B6HA 3AU5A 2RNRB 1ZC3B 1FHWA 2YSZA 1ZM0A 3WA0A 3A8QA 1U5EA 3GYOA 4GZUA 1OY2A 1BTNA 2YS3A 4MY6A 4DIXA 5JLJB 5LG4B 1MIZB 3SUZA 3V5WA 2DA0A 1UNQA 4YONA
chains in the Genus database with same CATH topology
4QJ4B 3TO1A 2B5RC 5D0QE 3D4EA 2KM7A 2GCJA 3FVCA 4OSNA 2PXGA 4KHBB 2G2UB 3TVVA 3GYPA 2YT2A 4OT1A 3E2LC 2GCLA 2Z13A 3C4OB 4PQ0A 4KHAA 3C7UB 3U12A 2GUMA 3NWAA 1XXMC 2G2WB 3FSSA 2YH9A 3E2KC 4GNKB 2K8EA 5I2MA 4KHBA 4IOYX 3A58A 4KHOA 3C7VB 3N4IB 4QJ3B 4QJ5B 2KXXA 3GMUB 2Z14A 3OHMB 5IRSA 1S0WC 2RRFA 2KR0A 4HSIA 5AYWE 2R2YA 2Z4DA 4GOUA 4Z2MB 4IFSA 1JTGB 2K49A 5EKQE 2FJUB 4QXAB 3HIEA 4CSQA 5M4YB 4L1RA 2KUQA 5D0OE 2ZKMX 3TW1A 3NWFA 4Z2NA 4DM5A 3NWDA 3C4PB 3NW8A 3GYOA 1ZYIA 2NBVA 4D6WA 4DIXA 5LG4B 2KIGA 5I2SA 2KIEA 2Z59A
chains in the Genus database with same CATH homology


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