2GBWA

Crystal structure of biphenyl 2,3-dioxygenase from sphingomonas yanoikuyae b1
Total Genus 150
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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
150
sequence length
449
structure length
449
Chain Sequence
b'TLVDTVNASQSRQVFWDEDVYALEIERIFSRAWLMLGHESLVPKPGDFITTYMAEDKVILSHQSDGTFRAFINSCSHRGNQICHADSGNAKAFVCNYHGWVFGQDGSLVDVPLESRCYHNSLDKQKLAAKSVRVETYKGFIFGCHDPEAPSLEDYLGEFRYYLDTIWEGAGGGMELLGPPMKSLLQCNWKVPAENFIGDGYHVGWTHAAALSQIGGELAGLAGNRADIPFDDLGLQFTTRHGHGFGVIDNAAAGLHIKREGWTKFLEDTRGEVRRKFGPERERLYLGHWNCSIFPNCSFLYGTNTFKIWHPRGPHEIEVWTYTIVPRDADPATKSMIQREAIRTFGTAGTLESDDGENMSSATYINRGVITRNGRMNSTMGVGYEGPHPVYPGIVGISFIGETSYRGFYRFWKEMIDAPDWASVKANDDTWDSVFPNRNFWNEKLNAAE'
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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.

molecule keywords Biphenyl 2,3-Dioxygenase Alpha Subunit
publication title Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
pubmed doi rcsb
source organism Sphingobium yanoikuyae
molecule tags Oxidoreductase
total genus 150
structure length 449
sequence length 449
chains with identical sequence C, E
ec nomenclature
pdb deposition date 2006-03-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00355 Rieske Rieske [2Fe-2S] domain
A PF00848 Ring_hydroxyl_A Ring hydroxylating alpha subunit (catalytic domain)
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domain 2gbwA02
3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 2gbwA01
4PV1D 2DE7D 2IBZE 2QJYC 2XSOA 2HMNA 2DE5D 2FYNC 1O7PA 3H1HE 4HM0A 1Z01A 3GL2A 1WQLA 2YFIA 1PPJE 2JO6A 4OGQD 1NTME 1G8JB 3L71E 2HMKA 3D89A 1JM1A 1O7GA 1BE3E 5KLVE 2E4PA 4AAYB 2YIUC 3GZYA 3L73E 3VMIA 1G8KB 4AIVA 3DQYA 5BOKA 1L0NE 2QJPC 3GZXA 3EN1A 3H1LE 3GKEA 3EQQA 2CKFA 2E75D 2NVEA 1PP9E 2ZYLA 1SQQE 4NBBA 2HMLA 1Z03A 4HM1A 2HMJA 1NTZE 2B24A 3GB4A 4H13D 3VMID 4NBAA 4QUPA 2BMQA 1WW9A 2NWFA 4QDDA 4HM3A 1Z02A 4NBGA 4NBEA 5AEUA 4NBCA 4HM8A 3GCEA 3AZCA 2DE6A 4HM7A 1NYKA 3H1JE 3VCAA 3H1IE 4NBBD 4NB8A 4PD4E 1BCCE 1EZVE 4NBAD 2FYUE 4U3FE 2GBWA 2B1XA 4NBDA 4NBED 1L0LE 4QCKA 2I7FA 2D2CD 2Q3WA 4NBCD 5AEWA 2DE6D 5KKZC 3VMHA 3L72E 4NB8D 1SQVE 3GTSA 2BCCE 1NTKE 3CWBE 1UUVA 2QPZA 3H1KE 2E74D 3CXHE 4QDCA 4NBDD 4HJLA 2YVJB 2BMOA 4EMJB 1RIEA 2XSHA 3VCPA 4NBFA 1SQPE 1O7NA 4QUQA 2A06E 2QJKC 4H0LD 1O7HA 3GTEA 1NDOA 1SQBE 2JZAA 4HKVA 4HM6A 3FOUA 4NB9A 1VCKA 2NVGA 4HM5A 2XRXA 1KB9E 1SJGA 1VF5D 4NBGD 3C0DA 4P1BH 3GCFA 4NBHA 2BMRA 3TGUE 1P84E 2NVFA 1ZRTE 3N0QA 2YFJA 3CX5E 1EG9A 2NUMA 4HM2A 3GKQA 1SQXE 3BCCE 4NB9D 2HMMA 1RFSA 2GBXA 4QDFA 5HL4A 4P1CH 4NBHD 2YFLA 2NUKA 1ULIA 1KYOE 3L70E 1O7WA 5CXMA 3VMHD 1FQTA 1NU1E 5KLIC 3VMGA 1VM9A 1ULJA 2DE7A 4QDFB 3GL0A 2DE5A 1Q90C 1UUWA 2ZT9D 4H44D 3GOBA 4HM4A 2HMOA 2XR8A 3L75E 3L74E 4QURA 3VMGD 1O7MA 2E76D 4NBFD 2E4QA
chains in the Genus database with same CATH superfamily
4PV1D 2DE7D 2IBZE 2QJYC 2XSOA 2HMNA 2DE5D 2FYNC 1O7PA 3H1HE 4HM0A 1Z01A 3GL2A 1WQLA 2YFIA 1PPJE 2JO6A 4OGQD 1NTME 1G8JB 3L71E 2HMKA 3D89A 1JM1A 1O7GA 1BE3E 5KLVE 2E4PA 4AAYB 2YIUC 3GZYA 3L73E 3VMIA 1G8KB 4AIVA 3DQYA 5BOKA 1L0NE 2QJPC 3GZXA 3EN1A 3H1LE 3GKEA 3EQQA 2CKFA 2E75D 2NVEA 1PP9E 2ZYLA 1SQQE 4NBBA 2HMLA 1Z03A 4HM1A 2HMJA 1NTZE 2B24A 3GB4A 4H13D 3VMID 4NBAA 4QUPA 2BMQA 1WW9A 2NWFA 4QDDA 4HM3A 1Z02A 4NBGA 4NBEA 5AEUA 4NBCA 4HM8A 3GCEA 3AZCA 2DE6A 4HM7A 1NYKA 3H1JE 3VCAA 3H1IE 4NBBD 4NB8A 4PD4E 1BCCE 1EZVE 4NBAD 2FYUE 4U3FE 2GBWA 2B1XA 4NBDA 4NBED 1L0LE 4QCKA 2I7FA 2D2CD 2Q3WA 4NBCD 5AEWA 2DE6D 5KKZC 3VMHA 3L72E 4NB8D 1SQVE 3GTSA 2BCCE 1NTKE 3CWBE 1UUVA 2QPZA 3H1KE 2E74D 3CXHE 4QDCA 4NBDD 4HJLA 2YVJB 2BMOA 4EMJB 1RIEA 2XSHA 3VCPA 4NBFA 1SQPE 1O7NA 4QUQA 2A06E 2QJKC 4H0LD 1O7HA 3GTEA 1NDOA 1SQBE 2JZAA 4HKVA 4HM6A 3FOUA 4NB9A 1VCKA 2NVGA 4HM5A 2XRXA 1KB9E 1SJGA 1VF5D 4NBGD 3C0DA 4P1BH 3GCFA 4NBHA 2BMRA 3TGUE 1P84E 2NVFA 1ZRTE 3N0QA 2YFJA 3CX5E 1EG9A 2NUMA 4HM2A 3GKQA 1SQXE 3BCCE 4NB9D 2HMMA 1RFSA 2GBXA 4QDFA 5HL4A 4P1CH 4NBHD 2YFLA 2NUKA 1ULIA 1KYOE 3L70E 1O7WA 5CXMA 3VMHD 1FQTA 1NU1E 5KLIC 3VMGA 1VM9A 1ULJA 2DE7A 4QDFB 3GL0A 2DE5A 1Q90C 1UUWA 2ZT9D 4H44D 3GOBA 4HM4A 2HMOA 2XR8A 3L75E 3L74E 4QURA 3VMGD 1O7MA 2E76D 4NBFD 2E4QA
chains in the Genus database with same CATH topology
4PV1D 2DE7D 2IBZE 2QJYC 2XSOA 2HMNA 2DE5D 2FYNC 1O7PA 3H1HE 4HM0A 1Z01A 3GL2A 1WQLA 2YFIA 1PPJE 2JO6A 4OGQD 1NTME 1G8JB 3L71E 2HMKA 3D89A 1JM1A 1O7GA 1BE3E 5KLVE 2E4PA 4AAYB 2YIUC 3GZYA 3L73E 3VMIA 1G8KB 4AIVA 3DQYA 5BOKA 1L0NE 2QJPC 3GZXA 3EN1A 3H1LE 3GKEA 3EQQA 2CKFA 2E75D 2NVEA 1PP9E 2ZYLA 1SQQE 4NBBA 2HMLA 1Z03A 4HM1A 2HMJA 1NTZE 2B24A 3GB4A 4H13D 3VMID 4NBAA 4QUPA 2BMQA 1WW9A 2NWFA 4QDDA 4HM3A 1Z02A 4NBGA 4NBEA 5AEUA 4NBCA 4HM8A 3GCEA 3AZCA 2DE6A 4HM7A 1NYKA 3H1JE 3VCAA 3H1IE 4NBBD 4NB8A 4PD4E 1BCCE 1EZVE 4NBAD 2FYUE 4U3FE 2GBWA 2B1XA 4NBDA 4NBED 1L0LE 4QCKA 2I7FA 2D2CD 2Q3WA 4NBCD 5AEWA 2DE6D 5KKZC 3VMHA 3L72E 4NB8D 1SQVE 3GTSA 2BCCE 1NTKE 3CWBE 1UUVA 2QPZA 3H1KE 2E74D 3CXHE 4QDCA 4NBDD 4HJLA 2YVJB 2BMOA 4EMJB 1RIEA 2XSHA 3VCPA 4NBFA 1SQPE 1O7NA 4QUQA 2A06E 2QJKC 4H0LD 1O7HA 3GTEA 1NDOA 1SQBE 2JZAA 4HKVA 4HM6A 3FOUA 4NB9A 1VCKA 2NVGA 4HM5A 2XRXA 1KB9E 1SJGA 1VF5D 4NBGD 3C0DA 4P1BH 3GCFA 4NBHA 2BMRA 3TGUE 1P84E 2NVFA 1ZRTE 3N0QA 2YFJA 3CX5E 1EG9A 2NUMA 4HM2A 3GKQA 1SQXE 3BCCE 4NB9D 2HMMA 1RFSA 2GBXA 4QDFA 5HL4A 4P1CH 4NBHD 2YFLA 2NUKA 1ULIA 1KYOE 3L70E 1O7WA 5CXMA 3VMHD 1FQTA 1NU1E 5KLIC 3VMGA 1VM9A 1ULJA 2DE7A 4QDFB 3GL0A 2DE5A 1Q90C 1UUWA 2ZT9D 4H44D 3GOBA 4HM4A 2HMOA 2XR8A 3L75E 3L74E 4QURA 3VMGD 1O7MA 2E76D 4NBFD 2E4QA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4PV1 D;  2DE7 D;  2IBZ E;  2QJY C;  2XSO A;  2HMN A;  2DE5 D;  2FYN C;  1O7P A;  3H1H E;  4HM0 A;  1Z01 A;  3GL2 A;  1WQL A;  2YFI A;  1PPJ E;  2JO6 A;  4OGQ D;  1NTM E;  1G8J B;  3L71 E;  2HMK A;  3D89 A;  1JM1 A;  1O7G A;  1BE3 E;  5KLV E;  2E4P A;  4AAY B;  2YIU C;  3GZY A;  3L73 E;  3VMI A;  1G8K B;  4AIV A;  3DQY A;  5BOK A;  1L0N E;  2QJP C;  3GZX A;  3EN1 A;  3H1L E;  3GKE A;  3EQQ A;  2CKF A;  2E75 D;  2NVE A;  1PP9 E;  2ZYL A;  1SQQ E;  4NBB A;  2HML A;  1Z03 A;  4HM1 A;  2HMJ A;  1NTZ E;  2B24 A;  3GB4 A;  4H13 D;  3VMI D;  4NBA A;  4QUP A;  2BMQ A;  1WW9 A;  2NWF A;  4QDD A;  4HM3 A;  1Z02 A;  4NBG A;  4NBE A;  5AEU A;  4NBC A;  4HM8 A;  3GCE A;  3AZC A;  2DE6 A;  4HM7 A;  1NYK A;  3H1J E;  3VCA A;  3H1I E;  4NBB D;  4NB8 A;  4PD4 E;  1BCC E;  1EZV E;  4NBA D;  2FYU E;  4U3F E;  2GBW A;  2B1X A;  4NBD A;  4NBE D;  1L0L E;  4QCK A;  2I7F A;  2D2C D;  2Q3W A;  4NBC D;  5AEW A;  2DE6 D;  5KKZ C;  3VMH A;  3L72 E;  4NB8 D;  1SQV E;  3GTS A;  2BCC E;  1NTK E;  3CWB E;  1UUV A;  2QPZ A;  3H1K E;  2E74 D;  3CXH E;  4QDC A;  4NBD D;  4HJL A;  2YVJ B;  2BMO A;  4EMJ B;  1RIE A;  2XSH A;  3VCP A;  4NBF A;  1SQP E;  1O7N A;  4QUQ A;  2A06 E;  2QJK C;  4H0L D;  1O7H A;  3GTE A;  1NDO A;  1SQB E;  2JZA A;  4HKV A;  4HM6 A;  3FOU A;  4NB9 A;  1VCK A;  2NVG A;  4HM5 A;  2XRX A;  1KB9 E;  1SJG A;  1VF5 D;  4NBG D;  3C0D A;  4P1B H;  3GCF A;  4NBH A;  2BMR A;  3TGU E;  1P84 E;  2NVF A;  1ZRT E;  3N0Q A;  2YFJ A;  3CX5 E;  1EG9 A;  2NUM A;  4HM2 A;  3GKQ A;  1SQX E;  3BCC E;  4NB9 D;  2HMM A;  1RFS A;  2GBX A;  4QDF A;  5HL4 A;  4P1C H;  4NBH D;  2YFL A;  2NUK A;  1ULI A;  1KYO E;  3L70 E;  1O7W A;  5CXM A;  3VMH D;  1FQT A;  1NU1 E;  5KLI C;  3VMG A;  1VM9 A;  1ULJ A;  2DE7 A;  4QDF B;  3GL0 A;  2DE5 A;  1Q90 C;  1UUW A;  2ZT9 D;  4H44 D;  3GOB A;  4HM4 A;  2HMO A;  2XR8 A;  3L75 E;  3L74 E;  4QUR A;  3VMG D;  1O7M A;  2E76 D;  4NBF D;  2E4Q A; 
#chains in the Genus database with same CATH topology
 4PV1 D;  2DE7 D;  2IBZ E;  2QJY C;  2XSO A;  2HMN A;  2DE5 D;  2FYN C;  1O7P A;  3H1H E;  4HM0 A;  1Z01 A;  3GL2 A;  1WQL A;  2YFI A;  1PPJ E;  2JO6 A;  4OGQ D;  1NTM E;  1G8J B;  3L71 E;  2HMK A;  3D89 A;  1JM1 A;  1O7G A;  1BE3 E;  5KLV E;  2E4P A;  4AAY B;  2YIU C;  3GZY A;  3L73 E;  3VMI A;  1G8K B;  4AIV A;  3DQY A;  5BOK A;  1L0N E;  2QJP C;  3GZX A;  3EN1 A;  3H1L E;  3GKE A;  3EQQ A;  2CKF A;  2E75 D;  2NVE A;  1PP9 E;  2ZYL A;  1SQQ E;  4NBB A;  2HML A;  1Z03 A;  4HM1 A;  2HMJ A;  1NTZ E;  2B24 A;  3GB4 A;  4H13 D;  3VMI D;  4NBA A;  4QUP A;  2BMQ A;  1WW9 A;  2NWF A;  4QDD A;  4HM3 A;  1Z02 A;  4NBG A;  4NBE A;  5AEU A;  4NBC A;  4HM8 A;  3GCE A;  3AZC A;  2DE6 A;  4HM7 A;  1NYK A;  3H1J E;  3VCA A;  3H1I E;  4NBB D;  4NB8 A;  4PD4 E;  1BCC E;  1EZV E;  4NBA D;  2FYU E;  4U3F E;  2GBW A;  2B1X A;  4NBD A;  4NBE D;  1L0L E;  4QCK A;  2I7F A;  2D2C D;  2Q3W A;  4NBC D;  5AEW A;  2DE6 D;  5KKZ C;  3VMH A;  3L72 E;  4NB8 D;  1SQV E;  3GTS A;  2BCC E;  1NTK E;  3CWB E;  1UUV A;  2QPZ A;  3H1K E;  2E74 D;  3CXH E;  4QDC A;  4NBD D;  4HJL A;  2YVJ B;  2BMO A;  4EMJ B;  1RIE A;  2XSH A;  3VCP A;  4NBF A;  1SQP E;  1O7N A;  4QUQ A;  2A06 E;  2QJK C;  4H0L D;  1O7H A;  3GTE A;  1NDO A;  1SQB E;  2JZA A;  4HKV A;  4HM6 A;  3FOU A;  4NB9 A;  1VCK A;  2NVG A;  4HM5 A;  2XRX A;  1KB9 E;  1SJG A;  1VF5 D;  4NBG D;  3C0D A;  4P1B H;  3GCF A;  4NBH A;  2BMR A;  3TGU E;  1P84 E;  2NVF A;  1ZRT E;  3N0Q A;  2YFJ A;  3CX5 E;  1EG9 A;  2NUM A;  4HM2 A;  3GKQ A;  1SQX E;  3BCC E;  4NB9 D;  2HMM A;  1RFS A;  2GBX A;  4QDF A;  5HL4 A;  4P1C H;  4NBH D;  2YFL A;  2NUK A;  1ULI A;  1KYO E;  3L70 E;  1O7W A;  5CXM A;  3VMH D;  1FQT A;  1NU1 E;  5KLI C;  3VMG A;  1VM9 A;  1ULJ A;  2DE7 A;  4QDF B;  3GL0 A;  2DE5 A;  1Q90 C;  1UUW A;  2ZT9 D;  4H44 D;  3GOB A;  4HM4 A;  2HMO A;  2XR8 A;  3L75 E;  3L74 E;  4QUR A;  3VMG D;  1O7M A;  2E76 D;  4NBF D;  2E4Q A; 
#chains in the Genus database with same CATH homology
 4PV1 D;  2DE7 D;  2IBZ E;  2QJY C;  2XSO A;  2HMN A;  2DE5 D;  2FYN C;  1O7P A;  3H1H E;  4HM0 A;  1Z01 A;  3GL2 A;  1WQL A;  2YFI A;  1PPJ E;  2JO6 A;  4OGQ D;  1NTM E;  1G8J B;  3L71 E;  2HMK A;  3D89 A;  1JM1 A;  1O7G A;  1BE3 E;  5KLV E;  2E4P A;  4AAY B;  2YIU C;  3GZY A;  3L73 E;  3VMI A;  1G8K B;  4AIV A;  3DQY A;  5BOK A;  1L0N E;  2QJP C;  3GZX A;  3EN1 A;  3H1L E;  3GKE A;  3EQQ A;  2CKF A;  2E75 D;  2NVE A;  1PP9 E;  2ZYL A;  1SQQ E;  4NBB A;  2HML A;  1Z03 A;  4HM1 A;  2HMJ A;  1NTZ E;  2B24 A;  3GB4 A;  4H13 D;  3VMI D;  4NBA A;  4QUP A;  2BMQ A;  1WW9 A;  2NWF A;  4QDD A;  4HM3 A;  1Z02 A;  4NBG A;  4NBE A;  5AEU A;  4NBC A;  4HM8 A;  3GCE A;  3AZC A;  2DE6 A;  4HM7 A;  1NYK A;  3H1J E;  3VCA A;  3H1I E;  4NBB D;  4NB8 A;  4PD4 E;  1BCC E;  1EZV E;  4NBA D;  2FYU E;  4U3F E;  2GBW A;  2B1X A;  4NBD A;  4NBE D;  1L0L E;  4QCK A;  2I7F A;  2D2C D;  2Q3W A;  4NBC D;  5AEW A;  2DE6 D;  5KKZ C;  3VMH A;  3L72 E;  4NB8 D;  1SQV E;  3GTS A;  2BCC E;  1NTK E;  3CWB E;  1UUV A;  2QPZ A;  3H1K E;  2E74 D;  3CXH E;  4QDC A;  4NBD D;  4HJL A;  2YVJ B;  2BMO A;  4EMJ B;  1RIE A;  2XSH A;  3VCP A;  4NBF A;  1SQP E;  1O7N A;  4QUQ A;  2A06 E;  2QJK C;  4H0L D;  1O7H A;  3GTE A;  1NDO A;  1SQB E;  2JZA A;  4HKV A;  4HM6 A;  3FOU A;  4NB9 A;  1VCK A;  2NVG A;  4HM5 A;  2XRX A;  1KB9 E;  1SJG A;  1VF5 D;  4NBG D;  3C0D A;  4P1B H;  3GCF A;  4NBH A;  2BMR A;  3TGU E;  1P84 E;  2NVF A;  1ZRT E;  3N0Q A;  2YFJ A;  3CX5 E;  1EG9 A;  2NUM A;  4HM2 A;  3GKQ A;  1SQX E;  3BCC E;  4NB9 D;  2HMM A;  1RFS A;  2GBX A;  4QDF A;  5HL4 A;  4P1C H;  4NBH D;  2YFL A;  2NUK A;  1ULI A;  1KYO E;  3L70 E;  1O7W A;  5CXM A;  3VMH D;  1FQT A;  1NU1 E;  5KLI C;  3VMG A;  1VM9 A;  1ULJ A;  2DE7 A;  4QDF B;  3GL0 A;  2DE5 A;  1Q90 C;  1UUW A;  2ZT9 D;  4H44 D;  3GOB A;  4HM4 A;  2HMO A;  2XR8 A;  3L75 E;  3L74 E;  4QUR A;  3VMG D;  1O7M A;  2E76 D;  4NBF D;  2E4Q 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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