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


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