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
Loading diagram...

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.

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


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