2YFIA

Crystal structure of biphenyl dioxygenase variant rr41 (bpdo-rr41)
Total Genus 135
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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
135
sequence length
442
structure length
433
Chain Sequence
NWTPEAIRGLVDQEKGLLDPRIYADQSLYELELERVFGRSWLLLGHESHVPETGDFLATYMGEDPVVMVRQKDKSIKVFLNQCRHRGMRICRSDAGNAKAFTCSYHGWAYDIAGKLVNVPFEKEAFFDKAEWGPLQARVATYKGLVFANWDVQAPDLETYLGDARPYMDVMLDRTPAGTVAIGGMQKWVIPCNWKFAAEQFCSDMYHAGTTTHLSGILAGIPPEMDLSQAQIPTKGNQFRAAWGGHGSGWYVDEPGSLLAVMGPKVTQYWTEGPAAELAEQRLGHTGMPVRRMVGQHMTIFPTCSFLPAMNQIRVWHPRGPNEIEVWAFTLVDADAPAEIKEEYRRHNIRNFSAGGVFEQDDGENWVEIQKGLRGYKAKSQPFNAQMGLGRSQTGHPDFPGNVGYVYAEEAARGMYHHWMRMMSEPSWATLKP
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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 DIOXYGENASE SUBUNIT ALPHA
publication title Retuning Rieske-Type Oxygenases to Expand Substrate Range.
pubmed doi rcsb
source organism Burkholderia xenovorans
molecule tags Oxidoreductase
total genus 135
structure length 433
sequence length 442
chains with identical sequence C, E, G, I, K
ec nomenclature ec 1.14.12.18: Biphenyl 2,3-dioxygenase.
pdb deposition date 2011-04-06

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 2yfiA02
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 2yfiA01
4HM4A 3CWBE 2XR8A 3AZCA 4NB9A 2FYUE 3VMGD 3GTEA 1G8JB 4EMJB 4H0LD 2BMQA 2HMMA 3GTSA 3TGUE 2NVGA 5HL4A 4P1CH 4U3FE 5AEUA 1NTME 2I7FA 2QJPC 3VMGA 2E74D 2GBWA 2XRXA 2DE6D 1NTZE 1VF5D 2B1XA 2HMKA 1WQLA 1NU1E 3BCCE 3EQQA 1Z03A 1L0LE 3H1JE 4HM3A 2HMOA 3VMID 3H1KE 4NB9D 1NDOA 3GB4A 4HM1A 2HMLA 1SQVE 3GCFA 1O7PA 2Q3WA 4QUPA 2GBXA 1VCKA 3GL2A 3VCAA 3N0QA 1G8KB 3VMIA 2YFJA 5BOKA 1UUWA 3GZXA 4OGQD 2NWFA 3GKQA 4QDFA 1PP9E 4HM8A 1ZRTE 1KB9E 4QUQA 3L71E 1SJGA 1JM1A 2NVFA 4NB8A 1ULJA 1SQPE 2YIUC 1Z01A 4QCKA 3GL0A 2QJYC 5CXMA 3CX5E 1O7MA 1SQBE 3GOBA 1VM9A 1NTKE 2NVEA 4NBHD 2D2CD 1KYOE 2QPZA 3H1HE 2BCCE 3GKEA 4HM5A 4AAYB 3L75E 1EG9A 3DQYA 3L72E 5AEWA 2NUMA 2YFIA 1NYKA 4HKVA 1PPJE 4NBDD 3VMHA 3L73E 2JZAA 3GZYA 4PV1D 4AIVA 5KLVE 4NBHA 2ZYLA 2QJKC 1P84E 4NB8D 2E4QA 4HM7A 2NUKA 2IBZE 1L0NE 4PD4E 4NBBA 4NBDA 2HMJA 4QURA 1BCCE 3C0DA 1O7NA 3GCEA 2DE7A 1FQTA 1O7GA 1WW9A 2DE5A 2B24A 2E75D 1O7HA 5KLIC 4H44D 3H1LE 4NBFA 4NBEA 4QDCA 3VMHD 1EZVE 4HM6A 4P1BH 2JO6A 2A06E 3D89A 4H13D 1BE3E 1Q90C 4HM0A 4HM2A 3CXHE 2E76D 4QDDA 2YFLA 4NBGA 5KKZC 1RIEA 2CKFA 4NBBD 2BMOA 4NBCA 2ZT9D 4NBAA 2DE7D 1RFSA 4QDFB 2DE5D 3L74E 1O7WA 2E4PA 2BMRA 3EN1A 2XSOA 4NBFD 4NBED 2FYNC 1ULIA 3VCPA 2YVJB 2HMNA 3FOUA 3H1IE 1SQXE 1Z02A 1SQQE 4HJLA 4NBGD 1UUVA 2DE6A 2XSHA 3L70E 4NBCD 4NBAD
chains in the Genus database with same CATH superfamily
4HM4A 3CWBE 2XR8A 3AZCA 4NB9A 2FYUE 3VMGD 3GTEA 1G8JB 4EMJB 4H0LD 2BMQA 2HMMA 3GTSA 3TGUE 2NVGA 5HL4A 4P1CH 4U3FE 5AEUA 1NTME 2I7FA 2QJPC 3VMGA 2E74D 2GBWA 2XRXA 2DE6D 1NTZE 1VF5D 2B1XA 2HMKA 1WQLA 1NU1E 3BCCE 3EQQA 1Z03A 1L0LE 3H1JE 4HM3A 2HMOA 3VMID 3H1KE 4NB9D 1NDOA 3GB4A 4HM1A 2HMLA 1SQVE 3GCFA 1O7PA 2Q3WA 4QUPA 2GBXA 1VCKA 3GL2A 3VCAA 3N0QA 1G8KB 3VMIA 2YFJA 5BOKA 1UUWA 3GZXA 4OGQD 2NWFA 3GKQA 4QDFA 1PP9E 4HM8A 1ZRTE 1KB9E 4QUQA 3L71E 1SJGA 1JM1A 2NVFA 4NB8A 1ULJA 1SQPE 2YIUC 1Z01A 4QCKA 3GL0A 2QJYC 5CXMA 3CX5E 1O7MA 1SQBE 3GOBA 1VM9A 1NTKE 2NVEA 4NBHD 2D2CD 1KYOE 2QPZA 3H1HE 2BCCE 3GKEA 4HM5A 4AAYB 3L75E 1EG9A 3DQYA 3L72E 5AEWA 2NUMA 2YFIA 1NYKA 4HKVA 1PPJE 4NBDD 3VMHA 3L73E 2JZAA 3GZYA 4PV1D 4AIVA 5KLVE 4NBHA 2ZYLA 2QJKC 1P84E 4NB8D 2E4QA 4HM7A 2NUKA 2IBZE 1L0NE 4PD4E 4NBBA 4NBDA 2HMJA 4QURA 1BCCE 3C0DA 1O7NA 3GCEA 2DE7A 1FQTA 1O7GA 1WW9A 2DE5A 2B24A 2E75D 1O7HA 5KLIC 4H44D 3H1LE 4NBFA 4NBEA 4QDCA 3VMHD 1EZVE 4HM6A 4P1BH 2JO6A 2A06E 3D89A 4H13D 1BE3E 1Q90C 4HM0A 4HM2A 3CXHE 2E76D 4QDDA 2YFLA 4NBGA 5KKZC 1RIEA 2CKFA 4NBBD 2BMOA 4NBCA 2ZT9D 4NBAA 2DE7D 1RFSA 4QDFB 2DE5D 3L74E 1O7WA 2E4PA 2BMRA 3EN1A 2XSOA 4NBFD 4NBED 2FYNC 1ULIA 3VCPA 2YVJB 2HMNA 3FOUA 3H1IE 1SQXE 1Z02A 1SQQE 4HJLA 4NBGD 1UUVA 2DE6A 2XSHA 3L70E 4NBCD 4NBAD
chains in the Genus database with same CATH topology
4HM4A 3CWBE 2XR8A 3AZCA 4NB9A 2FYUE 3VMGD 3GTEA 1G8JB 4EMJB 4H0LD 2BMQA 2HMMA 3GTSA 3TGUE 2NVGA 5HL4A 4P1CH 4U3FE 5AEUA 1NTME 2I7FA 2QJPC 3VMGA 2E74D 2GBWA 2XRXA 2DE6D 1NTZE 1VF5D 2B1XA 2HMKA 1WQLA 1NU1E 3BCCE 3EQQA 1Z03A 1L0LE 3H1JE 4HM3A 2HMOA 3VMID 3H1KE 4NB9D 1NDOA 3GB4A 4HM1A 2HMLA 1SQVE 3GCFA 1O7PA 2Q3WA 4QUPA 2GBXA 1VCKA 3GL2A 3VCAA 3N0QA 1G8KB 3VMIA 2YFJA 5BOKA 1UUWA 3GZXA 4OGQD 2NWFA 3GKQA 4QDFA 1PP9E 4HM8A 1ZRTE 1KB9E 4QUQA 3L71E 1SJGA 1JM1A 2NVFA 4NB8A 1ULJA 1SQPE 2YIUC 1Z01A 4QCKA 3GL0A 2QJYC 5CXMA 3CX5E 1O7MA 1SQBE 3GOBA 1VM9A 1NTKE 2NVEA 4NBHD 2D2CD 1KYOE 2QPZA 3H1HE 2BCCE 3GKEA 4HM5A 4AAYB 3L75E 1EG9A 3DQYA 3L72E 5AEWA 2NUMA 2YFIA 1NYKA 4HKVA 1PPJE 4NBDD 3VMHA 3L73E 2JZAA 3GZYA 4PV1D 4AIVA 5KLVE 4NBHA 2ZYLA 2QJKC 1P84E 4NB8D 2E4QA 4HM7A 2NUKA 2IBZE 1L0NE 4PD4E 4NBBA 4NBDA 2HMJA 4QURA 1BCCE 3C0DA 1O7NA 3GCEA 2DE7A 1FQTA 1O7GA 1WW9A 2DE5A 2B24A 2E75D 1O7HA 5KLIC 4H44D 3H1LE 4NBFA 4NBEA 4QDCA 3VMHD 1EZVE 4HM6A 4P1BH 2JO6A 2A06E 3D89A 4H13D 1BE3E 1Q90C 4HM0A 4HM2A 3CXHE 2E76D 4QDDA 2YFLA 4NBGA 5KKZC 1RIEA 2CKFA 4NBBD 2BMOA 4NBCA 2ZT9D 4NBAA 2DE7D 1RFSA 4QDFB 2DE5D 3L74E 1O7WA 2E4PA 2BMRA 3EN1A 2XSOA 4NBFD 4NBED 2FYNC 1ULIA 3VCPA 2YVJB 2HMNA 3FOUA 3H1IE 1SQXE 1Z02A 1SQQE 4HJLA 4NBGD 1UUVA 2DE6A 2XSHA 3L70E 4NBCD 4NBAD
chains in the Genus database with same CATH homology


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