2GBXA

Crystal structure of biphenyl 2,3-dioxygenase from sphingomonas yanoikuyae b1 bound to biphenyl
Total Genus 122
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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
122
sequence length
449
structure length
449
Chain Sequence
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 tags Oxidoreductase
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
total genus 122
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 2gbxA02
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 2gbxA01
2YFJA 4NBHD 5KLVE 1Z03A 2QJPC 4HM8A 3GCEA 1SJGA 3L74E 4HM7A 3C0DA 1NDOA 2GBWA 3L72E 5AEUA 5HL4A 2XSOA 3VMID 4NBAD 2BMRA 1VF5D 2E4QA 3BCCE 2HMOA 3VMIA 4NBAA 1P84E 3N0QA 1EG9A 1SQXE 1NTME 4NBBD 1UUVA 2E75D 1BCCE 3GTEA 2ZYLA 4QUQA 4NBBA 2BCCE 2QPZA 4HM1A 3L75E 4HKVA 1ULIA 4NBCD 1G8JB 4EMJB 2NVGA 3H1HE 3CWBE 3GL2A 2E74D 3GCFA 4NBDD 4NBCA 3L73E 1O7MA 1ULJA 4HM4A 3H1LE 4NBDA 4NBGD 3GZYA 4OGQD 5BOKA 2JZAA 4PV1D 4NBGA 2D2CD 2E76D 1KYOE 3CX5E 2YVJB 3EQQA 1WW9A 3FOUA 4HM0A 4QDFA 3GZXA 4PD4E 4QUPA 2HMJA 4H44D 4HM5A 1JM1A 4NB9A 2GBXA 4HM2A 1O7PA 1ZRTE 2ZT9D 2DE5A 1O7GA 1WQLA 1NU1E 1NTKE 2HMMA 4H0LD 2B1XA 3EN1A 1PPJE 2BMOA 4HM3A 4P1CH 4QDDA 3H1KE 4HM6A 1Q90C 4NB8D 1KB9E 3L70E 2NUMA 1SQVE 1Z02A 4H13D 1RIEA 2DE6A 4NB8A 2HMNA 2YFLA 1SQPE 3H1IE 1O7WA 1O7NA 5KLIC 3DQYA 3GKQA 2Q3WA 1O7HA 1FQTA 4AAYB 2DE7D 3TGUE 2BMQA 4NB9D 3VCPA 3AZCA 2DE7A 2DE5D 1BE3E 2HMLA 2E4PA 3GOBA 3VMGD 3D89A 1NTZE 5AEWA 1NYKA 2JO6A 3VMGA 3VMHA 3VCAA 1Z01A 2YFIA 4AIVA 2YIUC 1SQBE 2XSHA 2QJYC 2DE6D 3GL0A 3L71E 4HJLA 2NUKA 4NBHA 4NBEA 1PP9E 3GKEA 2FYUE 2A06E 4QURA 4U3FE 4P1BH 3GB4A 4QDCA 2B24A 3H1JE 4QCKA 1G8KB 1SQQE 3GTSA 4NBFD 1EZVE 2IBZE 2NVFA 4NBFA 4QDFB 1VM9A 1RFSA 2CKFA 2FYNC 2XRXA 5CXMA 5KKZC 1VCKA 2HMKA 1UUWA 3VMHD 1L0NE 2NVEA 2NWFA 2QJKC 2I7FA 2XR8A 3CXHE 1L0LE 4NBED
chains in the Genus database with same CATH superfamily
2YFJA 4NBHD 5KLVE 1Z03A 2QJPC 4HM8A 3GCEA 1SJGA 3L74E 4HM7A 3C0DA 1NDOA 2GBWA 3L72E 5AEUA 5HL4A 2XSOA 3VMID 4NBAD 2BMRA 1VF5D 2E4QA 3BCCE 2HMOA 3VMIA 4NBAA 1P84E 3N0QA 1EG9A 1SQXE 1NTME 4NBBD 1UUVA 2E75D 1BCCE 3GTEA 2ZYLA 4QUQA 4NBBA 2BCCE 2QPZA 4HM1A 3L75E 4HKVA 1ULIA 4NBCD 1G8JB 4EMJB 2NVGA 3H1HE 3CWBE 3GL2A 2E74D 3GCFA 4NBDD 4NBCA 3L73E 1O7MA 1ULJA 4HM4A 3H1LE 4NBDA 4NBGD 3GZYA 4OGQD 5BOKA 2JZAA 4PV1D 4NBGA 2D2CD 2E76D 1KYOE 3CX5E 2YVJB 3EQQA 1WW9A 3FOUA 4HM0A 4QDFA 3GZXA 4PD4E 4QUPA 2HMJA 4H44D 4HM5A 1JM1A 4NB9A 2GBXA 4HM2A 1O7PA 1ZRTE 2ZT9D 2DE5A 1O7GA 1WQLA 1NU1E 1NTKE 2HMMA 4H0LD 2B1XA 3EN1A 1PPJE 2BMOA 4HM3A 4P1CH 4QDDA 3H1KE 4HM6A 1Q90C 4NB8D 1KB9E 3L70E 2NUMA 1SQVE 1Z02A 4H13D 1RIEA 2DE6A 4NB8A 2HMNA 2YFLA 1SQPE 3H1IE 1O7WA 1O7NA 5KLIC 3DQYA 3GKQA 2Q3WA 1O7HA 1FQTA 4AAYB 2DE7D 3TGUE 2BMQA 4NB9D 3VCPA 3AZCA 2DE7A 2DE5D 1BE3E 2HMLA 2E4PA 3GOBA 3VMGD 3D89A 1NTZE 5AEWA 1NYKA 2JO6A 3VMGA 3VMHA 3VCAA 1Z01A 2YFIA 4AIVA 2YIUC 1SQBE 2XSHA 2QJYC 2DE6D 3GL0A 3L71E 4HJLA 2NUKA 4NBHA 4NBEA 1PP9E 3GKEA 2FYUE 2A06E 4QURA 4U3FE 4P1BH 3GB4A 4QDCA 2B24A 3H1JE 4QCKA 1G8KB 1SQQE 3GTSA 4NBFD 1EZVE 2IBZE 2NVFA 4NBFA 4QDFB 1VM9A 1RFSA 2CKFA 2FYNC 2XRXA 5CXMA 5KKZC 1VCKA 2HMKA 1UUWA 3VMHD 1L0NE 2NVEA 2NWFA 2QJKC 2I7FA 2XR8A 3CXHE 1L0LE 4NBED
chains in the Genus database with same CATH topology
2YFJA 4NBHD 5KLVE 1Z03A 2QJPC 4HM8A 3GCEA 1SJGA 3L74E 4HM7A 3C0DA 1NDOA 2GBWA 3L72E 5AEUA 5HL4A 2XSOA 3VMID 4NBAD 2BMRA 1VF5D 2E4QA 3BCCE 2HMOA 3VMIA 4NBAA 1P84E 3N0QA 1EG9A 1SQXE 1NTME 4NBBD 1UUVA 2E75D 1BCCE 3GTEA 2ZYLA 4QUQA 4NBBA 2BCCE 2QPZA 4HM1A 3L75E 4HKVA 1ULIA 4NBCD 1G8JB 4EMJB 2NVGA 3H1HE 3CWBE 3GL2A 2E74D 3GCFA 4NBDD 4NBCA 3L73E 1O7MA 1ULJA 4HM4A 3H1LE 4NBDA 4NBGD 3GZYA 4OGQD 5BOKA 2JZAA 4PV1D 4NBGA 2D2CD 2E76D 1KYOE 3CX5E 2YVJB 3EQQA 1WW9A 3FOUA 4HM0A 4QDFA 3GZXA 4PD4E 4QUPA 2HMJA 4H44D 4HM5A 1JM1A 4NB9A 2GBXA 4HM2A 1O7PA 1ZRTE 2ZT9D 2DE5A 1O7GA 1WQLA 1NU1E 1NTKE 2HMMA 4H0LD 2B1XA 3EN1A 1PPJE 2BMOA 4HM3A 4P1CH 4QDDA 3H1KE 4HM6A 1Q90C 4NB8D 1KB9E 3L70E 2NUMA 1SQVE 1Z02A 4H13D 1RIEA 2DE6A 4NB8A 2HMNA 2YFLA 1SQPE 3H1IE 1O7WA 1O7NA 5KLIC 3DQYA 3GKQA 2Q3WA 1O7HA 1FQTA 4AAYB 2DE7D 3TGUE 2BMQA 4NB9D 3VCPA 3AZCA 2DE7A 2DE5D 1BE3E 2HMLA 2E4PA 3GOBA 3VMGD 3D89A 1NTZE 5AEWA 1NYKA 2JO6A 3VMGA 3VMHA 3VCAA 1Z01A 2YFIA 4AIVA 2YIUC 1SQBE 2XSHA 2QJYC 2DE6D 3GL0A 3L71E 4HJLA 2NUKA 4NBHA 4NBEA 1PP9E 3GKEA 2FYUE 2A06E 4QURA 4U3FE 4P1BH 3GB4A 4QDCA 2B24A 3H1JE 4QCKA 1G8KB 1SQQE 3GTSA 4NBFD 1EZVE 2IBZE 2NVFA 4NBFA 4QDFB 1VM9A 1RFSA 2CKFA 2FYNC 2XRXA 5CXMA 5KKZC 1VCKA 2HMKA 1UUWA 3VMHD 1L0NE 2NVEA 2NWFA 2QJKC 2I7FA 2XR8A 3CXHE 1L0LE 4NBED
chains in the Genus database with same CATH homology


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