1RDVA

Rubredoxin from desulfovibrio vulgaris miyazaki f, trigonal crystal form
Total Genus 6
Loading diagram...

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
6
sequence length
52
structure length
52
Chain Sequence
MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA
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.

Chord Diagram
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
publication title Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.
pubmed doi rcsb
molecule tags Electron transfer
molecule keywords RUBREDOXIN
total genus 6
structure length 52
sequence length 52
ec nomenclature
pdb deposition date 1998-09-30

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00301 Rubredoxin Rubredoxin
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.20.28.10 Mainly Beta Single Sheet Rubrerythrin, domain 2 Rubrerythrin, domain 2 1rdvA00
4POFA 1R0GA 5AI2A 5RXNA 2QL0A 4ME3A 1B71A 4RXNA 1SMUA 1YUXA 3PZAA 1IROA 1QYBA 1R0HA 3RYGA 2PVEA 1LKOA 1CADA 2KKDA 4AR3A 1RB9A 2PVXA 1DX8A 1T9QA 1IRNA 2KN9A 1YK5A 2DSXA 1R0FA 3SS2A 1S30A 1B2OA 1SMWA 3QVDA 1H7VA 1LTLA 3RZ6A 1BE7A 7RXNA 5AI3A 1BFYA 1FHHA 3A44A 2M4YA 1LKPA 3KYWA 1IU6A 1S2ZA 3RZTA 4YWLA 1LKMA 1B2JA 1C09A 3PWFA 1QCVA 5IY0A 3MPSA 1FHMA 6RXNA 1E8JA 1RDVA 8RXNA 2GMGA 2HR5A 4AR5A 1JYBA 1NNQA 3KYXA 2VL6A 1T9PA 1YUZA 2MS3A 1BQ9A 1B13A 1R0IA 3KYYA 1IU5A 4TPUA 2RDVA 3KYUA 1CAAA 4YWMA 2K2DA 3KYVA 1VCXA 1ZRPA 1YK4A 1RWDA 4AR6A 4K9FA 1YV1A 1DVBA 2V3BB 4AR4A 1R0JA 1BRFA 1RYTA 1T9OA 1SMMA 2LCQA 1BQ8A 2PYAA 1RDGA 4POGA 1S24A
chains in the Genus database with same CATH superfamily
5AI2A 5RXNA 3M3YL 4ME3A 2PSMC 3PKIA 4AHXA 2ZIXA 3J7Z1 4LHNA 3HAXC 4UY81 4A3GL 2PVXA 1Y1VL 1T9QA 4A3CL 3SS2A 3QVDA 4Y7NL 2JA7L 3A44A 2XJQA 3H99A 3S1ML 3P8BA 2RFKB 3HOZL 1WJVA 4YWLA 1LKMA 2HVYC 1NXGA 5MFZA 1RDVA 4B8CD 4AHZA 3LWRB 2HR5A 2R92L 1Y1WL 2AQCA 4C3IL 1PFUA 4JAGA 2VL6A 1YUZA 1K83L 4XXBB 2NVTL 4A3IL 2JI3A 4AHWA 3S2DL 4TPUA 2E2JL 3HKZP 3KYUA 4V196 4A93L 5FLML 3PIP1 1VCXA 3S2HL 1RWDA 2M4VA 2CKAA 4A3EL 4K9FA 1YV1A 4XGHA 4A3LL 1BRFA 5C44L 2CR8A 2NVQL 1RDGA 3GTOL 2A68D 5M5YL 2XJUA 4RXNA 2NYDA 1SMUA 1YUXA 5MF6A 3HJWB 3PZAA 1QYBA 2AUSB 3B08B 1I3QL 3LWOB 4BY1L 2KKDA 4U671 5GAGc 4X6AL 1DX8A 3H9CA 3GTGL 1YK5A 2DSXA 1R0FA 2PMZP 4C3JL 2NVXL 3S1NL 4A3KL 7RXNA 2V0EA 4AHYA 3HOWL 2JA8L 1OWCA 2Z3QB 1VZIA 2M6PA 4TVMA 1S2ZA 3P2AA 3HOXL 1I6HL 5GAHc 1VZHA 1QCVA 3NFPI 5IY0A 1FHMA 1E8JA 3LNLA 3VPBE 3K7AL 4AR5A 3H3VM 3MQKB 1IW7D 1PFYA 2WAQP 1NNQA 2A6ED 2V0FA 4GS7D 1T9PA 5M3FL 2MS3A 5JVG1 4JAEA 3GTLL 3KYYA 5GADc 1IU5A 3M4OL 2RDVA 2C6AA 1CAAA 4A3JL 2WB1P 2Z3RB 4AI0A 4BBRL 5DM71 4AR6A 2E2HL 1RYQA 3HJYB 1TWGL 3LWPB 1DVBA 1R0JA 4JAFA 2J9UB 1SMMA 3S14L 1S24A 1TWFL 1R0GA 2APOB 2QL0A 5EIOC 3LPEB 2L0ZA 1B71A 4AI1A 1R0HA 3GTPL 1PFVA 3RZOL 3H0GL 4AR3A 2JA5L 4A3ML 1RB9A 3B0AB 1IRNA 2KN9A 4ZN1B 4G6BA 5IYDL 1B2OA 3MSUA 5FJ8L 1SMWA 1H7VA 1BE7A 3PIO1 5AI3A 2EY4E 1BFYA 2B63L 2NVYL 5JVH1 1SFOL 3FKIL 3S16L 1LKPA 3KYWA 3GTML 5H1Sc 3PO3L 3RZTA 5DM61 1C09A 1PZXA 1I50L 3PWFA 3ZG6A 2A69D 3I4ML 3MPSA 3J7Y1 3GTJL 3H97A 8RXNA 4E6YA 1ODHA 4AI2A 3WWNB 5K2ME 5IP9L 2AYJA 2H12A 3KYXA 2XJPA 1QQTA 3S1QL 4WFN1 2CKCA 2BE5D 5MFPA 1TWCL 4QIWP 2XJRA 4YWMA 3QQCE 4A3DL 1YK4A 3RZDL 3WWLA 2YU9L 2ERJA 4AR4A 3IU3I 1RYTA 3PL5A 4LHLA 3I4NL 4AI3A 1VZGA 4POFA 4Y52L 3HOVL 3S17L 3HOYL 5C3EL 1IROA 3RYGA 2PVEA 1LKOA 3H9BA 1CADA 4C3HL 2B5ID 5C4XL 5MGNA 1TWHL 4ZN3B 1TWAL 1S30A 1Z92B 5IP7L 2C6BA 2XJSA 4BBSL 2O5JD 3GTQL 1LTLA 3RZ6A 2JA6L 1FHHA 4C2M1 5M3ML 5M5XL 2JI1A 4JADA 2R7ZL 2M4YA 3LWQB 1OWBA 3FDJA 2M6OA 1IU6A 4A3BL 3JR7A 5AN9H 4BXXL 2VUML 1B2JA 6RXNA 2A6HD 3LWVB 3PO2L 2GMGA 2XJVA 4A3FL 5IYBL 2R93L 2XJTA 1R9TL 1JYBA 5GAEc 1WCML 2E2IL 1F4LA 1BQ9A 2JI2A 3K35A 1B13A 2ERSA 4BY7L 2PPTA 1R0IA 1P7PA 3PKJA 3CQZL 3S1RL 5MLC3 2K2DA 3KYVA 1ZRPA 1PFWA 4AYBP 3HOUL 5EINC 2V3BB 3GTKL 1T9OA 3S15L 5IYCL 2LCQA 1BQ8A 2Y0SP 1NXEA 2PYAA 5M5WL 5C4JL 4POGA
chains in the Genus database with same CATH topology
4POFA 1R0GA 5AI2A 5RXNA 2QL0A 5EIOC 2A68D 3LPEB 2L0ZA 2XJUA 1B71A 4ME3A 4RXNA 2NYDA 1SMUA 1YUXA 2PSMC 4AI1A 5MF6A 3PKIA 3PZAA 1IROA 1QYBA 4AHXA 2ZIXA 3J7Z1 1R0HA 4LHNA 3B08B 3RYGA 2PVEA 1LKOA 1CADA 2KKDA 4AR3A 4UY81 2B5ID 1RB9A 4U671 5GAGc 2PVXA 3B0AB 5MGNA 1DX8A 4ZN3B 1T9QA 1IRNA 2KN9A 1YK5A 4ZN1B 2DSXA 4G6BA 1R0FA 3SS2A 1S30A 1Z92B 1B2OA 3MSUA 1SMWA 2C6BA 2XJSA 3QVDA 2O5JD 1H7VA 1LTLA 3RZ6A 1BE7A 7RXNA 3PIO1 5AI3A 2V0EA 4AHYA 1BFYA 1FHHA 5JVH1 3A44A 2JI1A 2XJQA 4JADA 1OWCA 2M4YA 1OWBA 1LKPA 2Z3QB 3KYWA 5H1Sc 1VZIA 2M6PA 3P8BA 4TVMA 2PYAA 1WJVA 1IU6A 1S2ZA 2M6OA 3P2AA 3RZTA 4YWLA 1LKMA 5AN9H 1NXGA 5DM61 1B2JA 1C09A 5GAHc 3ZG6A 3PWFA 1VZHA 1QCVA 2A69D 3NFPI 5IY0A 3MPSA 5MFZA 1FHMA 6RXNA 1E8JA 3J7Y1 1RDVA 2A6HD 3LNLA 3VPBE 4B8CD 8RXNA 2GMGA 2XJVA 4AHZA 2HR5A 4E6YA 1ODHA 4AI2A 4AR5A 2XJTA 3WWNB 5K2ME 2AYJA 2H12A 1JYBA 5GAEc 1IW7D 1NNQA 4JAGA 3KYXA 2A6ED 2V0FA 2VL6A 2XJPA 4GS7D 1T9PA 1YUZA 2MS3A 4WFN1 2CKCA 1BQ9A 2JI2A 2BE5D 3K35A 4JAEA 1B13A 2ERSA 4XXBB 5JVG1 2PPTA 1R0IA 2JI3A 4AHWA 3KYYA 5GADc 5MFPA 1IU5A 4TPUA 2RDVA 3PKJA 2XJRA 3KYUA 4V196 2C6AA 5MLC3 1CAAA 4YWMA 3PIP1 2K2DA 3QQCE 3KYVA 1VCXA 2Z3RB 1ZRPA 4AI0A 1YK4A 1RWDA 2M4VA 2CKAA 5DM71 4AR6A 4K9FA 3WWLA 1RYQA 1YV1A 2ERJA 1DVBA 4XGHA 5EINC 2V3BB 4AR4A 1R0JA 3IU3I 1BRFA 1RYTA 4JAFA 1T9OA 4LHLA 2J9UB 1SMMA 2LCQA 1BQ8A 2CR8A 1NXEA 4AI3A 1VZGA 1RDGA 4POGA 1S24A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4POF A;  1R0G A;  5AI2 A;  5RXN A;  2QL0 A;  4ME3 A;  1B71 A;  4RXN A;  1SMU A;  1YUX A;  3PZA A;  1IRO A;  1QYB A;  1R0H A;  3RYG A;  2PVE A;  1LKO A;  1CAD A;  2KKD A;  4AR3 A;  1RB9 A;  2PVX A;  1DX8 A;  1T9Q A;  1IRN A;  2KN9 A;  1YK5 A;  2DSX A;  1R0F A;  3SS2 A;  1S30 A;  1B2O A;  1SMW A;  3QVD A;  1H7V A;  1LTL A;  3RZ6 A;  1BE7 A;  7RXN A;  5AI3 A;  1BFY A;  1FHH A;  3A44 A;  2M4Y A;  1LKP A;  3KYW A;  1IU6 A;  1S2Z A;  3RZT A;  4YWL A;  1LKM A;  1B2J A;  1C09 A;  3PWF A;  1QCV A;  5IY0 A;  3MPS A;  1FHM A;  6RXN A;  1E8J A;  1RDV A;  8RXN A;  2GMG A;  2HR5 A;  4AR5 A;  1JYB A;  1NNQ A;  3KYX A;  2VL6 A;  1T9P A;  1YUZ A;  2MS3 A;  1BQ9 A;  1B13 A;  1R0I A;  3KYY A;  1IU5 A;  4TPU A;  2RDV A;  3KYU A;  1CAA A;  4YWM A;  2K2D A;  3KYV A;  1VCX A;  1ZRP A;  1YK4 A;  1RWD A;  4AR6 A;  4K9F A;  1YV1 A;  1DVB A;  2V3B B;  4AR4 A;  1R0J A;  1BRF A;  1RYT A;  1T9O A;  1SMM A;  2LCQ A;  1BQ8 A;  2PYA A;  1RDG A;  4POG A;  1S24 A; 
#chains in the Genus database with same CATH topology
 5AI2 A;  5RXN A;  3M3Y L;  4ME3 A;  2PSM C;  3PKI A;  4AHX A;  2ZIX A;  3J7Z 1;  4LHN A;  3HAX C;  4UY8 1;  4A3G L;  2PVX A;  1Y1V L;  1T9Q A;  4A3C L;  3SS2 A;  3QVD A;  4Y7N L;  2JA7 L;  3A44 A;  2XJQ A;  3H99 A;  3S1M L;  3P8B A;  2RFK B;  3HOZ L;  1WJV A;  4YWL A;  1LKM A;  2HVY C;  1NXG A;  5MFZ A;  1RDV A;  4B8C D;  4AHZ A;  3LWR B;  2HR5 A;  2R92 L;  1Y1W L;  2AQC A;  4C3I L;  1PFU A;  4JAG A;  2VL6 A;  1YUZ A;  1K83 L;  4XXB B;  2NVT L;  4A3I L;  2JI3 A;  4AHW A;  3S2D L;  4TPU A;  2E2J L;  3HKZ P;  3KYU A;  4V19 6;  4A93 L;  5FLM L;  3PIP 1;  1VCX A;  3S2H L;  1RWD A;  2M4V A;  2CKA A;  4A3E L;  4K9F A;  1YV1 A;  4XGH A;  4A3L L;  1BRF A;  5C44 L;  2CR8 A;  2NVQ L;  1RDG A;  3GTO L;  2A68 D;  5M5Y L;  2XJU A;  4RXN A;  2NYD A;  1SMU A;  1YUX A;  5MF6 A;  3HJW B;  3PZA A;  1QYB A;  2AUS B;  3B08 B;  1I3Q L;  3LWO B;  4BY1 L;  2KKD A;  4U67 1;  5GAG c;  4X6A L;  1DX8 A;  3H9C A;  3GTG L;  1YK5 A;  2DSX A;  1R0F A;  2PMZ P;  4C3J L;  2NVX L;  3S1N L;  4A3K L;  7RXN A;  2V0E A;  4AHY A;  3HOW L;  2JA8 L;  1OWC A;  2Z3Q B;  1VZI A;  2M6P A;  4TVM A;  1S2Z A;  3P2A A;  3HOX L;  1I6H L;  5GAH c;  1VZH A;  1QCV A;  3NFP I;  5IY0 A;  1FHM A;  1E8J A;  3LNL A;  3VPB E;  3K7A L;  4AR5 A;  3H3V M;  3MQK B;  1IW7 D;  1PFY A;  2WAQ P;  1NNQ A;  2A6E D;  2V0F A;  4GS7 D;  1T9P A;  5M3F L;  2MS3 A;  5JVG 1;  4JAE A;  3GTL L;  3KYY A;  5GAD c;  1IU5 A;  3M4O L;  2RDV A;  2C6A A;  1CAA A;  4A3J L;  2WB1 P;  2Z3R B;  4AI0 A;  4BBR L;  5DM7 1;  4AR6 A;  2E2H L;  1RYQ A;  3HJY B;  1TWG L;  3LWP B;  1DVB A;  1R0J A;  4JAF A;  2J9U B;  1SMM A;  3S14 L;  1S24 A;  1TWF L;  1R0G A;  2APO B;  2QL0 A;  5EIO C;  3LPE B;  2L0Z A;  1B71 A;  4AI1 A;  1R0H A;  3GTP L;  1PFV A;  3RZO L;  3H0G L;  4AR3 A;  2JA5 L;  4A3M L;  1RB9 A;  3B0A B;  1IRN A;  2KN9 A;  4ZN1 B;  4G6B A;  5IYD L;  1B2O A;  3MSU A;  5FJ8 L;  1SMW A;  1H7V A;  1BE7 A;  3PIO 1;  5AI3 A;  2EY4 E;  1BFY A;  2B63 L;  2NVY L;  5JVH 1;  1SFO L;  3FKI L;  3S16 L;  1LKP A;  3KYW A;  3GTM L;  5H1S c;  3PO3 L;  3RZT A;  5DM6 1;  1C09 A;  1PZX A;  1I50 L;  3PWF A;  3ZG6 A;  2A69 D;  3I4M L;  3MPS A;  3J7Y 1;  3GTJ L;  3H97 A;  8RXN A;  4E6Y A;  1ODH A;  4AI2 A;  3WWN B;  5K2M E;  5IP9 L;  2AYJ A;  2H12 A;  3KYX A;  2XJP A;  1QQT A;  3S1Q L;  4WFN 1;  2CKC A;  2BE5 D;  5MFP A;  1TWC L;  4QIW P;  2XJR A;  4YWM A;  3QQC E;  4A3D L;  1YK4 A;  3RZD L;  3WWL A;  2YU9 L;  2ERJ A;  4AR4 A;  3IU3 I;  1RYT A;  3PL5 A;  4LHL A;  3I4N L;  4AI3 A;  1VZG A;  4POF A;  4Y52 L;  3HOV L;  3S17 L;  3HOY L;  5C3E L;  1IRO A;  3RYG A;  2PVE A;  1LKO A;  3H9B A;  1CAD A;  4C3H L;  2B5I D;  5C4X L;  5MGN A;  1TWH L;  4ZN3 B;  1TWA L;  1S30 A;  1Z92 B;  5IP7 L;  2C6B A;  2XJS A;  4BBS L;  2O5J D;  3GTQ L;  1LTL A;  3RZ6 A;  2JA6 L;  1FHH A;  4C2M 1;  5M3M L;  5M5X L;  2JI1 A;  4JAD A;  2R7Z L;  2M4Y A;  3LWQ B;  1OWB A;  3FDJ A;  2M6O A;  1IU6 A;  4A3B L;  3JR7 A;  5AN9 H;  4BXX L;  2VUM L;  1B2J A;  6RXN A;  2A6H D;  3LWV B;  3PO2 L;  2GMG A;  2XJV A;  4A3F L;  5IYB L;  2R93 L;  2XJT A;  1R9T L;  1JYB A;  5GAE c;  1WCM L;  2E2I L;  1F4L A;  1BQ9 A;  2JI2 A;  3K35 A;  1B13 A;  2ERS A;  4BY7 L;  2PPT A;  1R0I A;  1P7P A;  3PKJ A;  3CQZ L;  3S1R L;  5MLC 3;  2K2D A;  3KYV A;  1ZRP A;  1PFW A;  4AYB P;  3HOU L;  5EIN C;  2V3B B;  3GTK L;  1T9O A;  3S15 L;  5IYC L;  2LCQ A;  1BQ8 A;  2Y0S P;  1NXE A;  2PYA A;  5M5W L;  5C4J L;  4POG A; 
#chains in the Genus database with same CATH homology
 4POF A;  1R0G A;  5AI2 A;  5RXN A;  2QL0 A;  5EIO C;  2A68 D;  3LPE B;  2L0Z A;  2XJU A;  1B71 A;  4ME3 A;  4RXN A;  2NYD A;  1SMU A;  1YUX A;  2PSM C;  4AI1 A;  5MF6 A;  3PKI A;  3PZA A;  1IRO A;  1QYB A;  4AHX A;  2ZIX A;  3J7Z 1;  1R0H A;  4LHN A;  3B08 B;  3RYG A;  2PVE A;  1LKO A;  1CAD A;  2KKD A;  4AR3 A;  4UY8 1;  2B5I D;  1RB9 A;  4U67 1;  5GAG c;  2PVX A;  3B0A B;  5MGN A;  1DX8 A;  4ZN3 B;  1T9Q A;  1IRN A;  2KN9 A;  1YK5 A;  4ZN1 B;  2DSX A;  4G6B A;  1R0F A;  3SS2 A;  1S30 A;  1Z92 B;  1B2O A;  3MSU A;  1SMW A;  2C6B A;  2XJS A;  3QVD A;  2O5J D;  1H7V A;  1LTL A;  3RZ6 A;  1BE7 A;  7RXN A;  3PIO 1;  5AI3 A;  2V0E A;  4AHY A;  1BFY A;  1FHH A;  5JVH 1;  3A44 A;  2JI1 A;  2XJQ A;  4JAD A;  1OWC A;  2M4Y A;  1OWB A;  1LKP A;  2Z3Q B;  3KYW A;  5H1S c;  1VZI A;  2M6P A;  3P8B A;  4TVM A;  2PYA A;  1WJV A;  1IU6 A;  1S2Z A;  2M6O A;  3P2A A;  3RZT A;  4YWL A;  1LKM A;  5AN9 H;  1NXG A;  5DM6 1;  1B2J A;  1C09 A;  5GAH c;  3ZG6 A;  3PWF A;  1VZH A;  1QCV A;  2A69 D;  3NFP I;  5IY0 A;  3MPS A;  5MFZ A;  1FHM A;  6RXN A;  1E8J A;  3J7Y 1;  1RDV A;  2A6H D;  3LNL A;  3VPB E;  4B8C D;  8RXN A;  2GMG A;  2XJV A;  4AHZ A;  2HR5 A;  4E6Y A;  1ODH A;  4AI2 A;  4AR5 A;  2XJT A;  3WWN B;  5K2M E;  2AYJ A;  2H12 A;  1JYB A;  5GAE c;  1IW7 D;  1NNQ A;  4JAG A;  3KYX A;  2A6E D;  2V0F A;  2VL6 A;  2XJP A;  4GS7 D;  1T9P A;  1YUZ A;  2MS3 A;  4WFN 1;  2CKC A;  1BQ9 A;  2JI2 A;  2BE5 D;  3K35 A;  4JAE A;  1B13 A;  2ERS A;  4XXB B;  5JVG 1;  2PPT A;  1R0I A;  2JI3 A;  4AHW A;  3KYY A;  5GAD c;  5MFP A;  1IU5 A;  4TPU A;  2RDV A;  3PKJ A;  2XJR A;  3KYU A;  4V19 6;  2C6A A;  5MLC 3;  1CAA A;  4YWM A;  3PIP 1;  2K2D A;  3QQC E;  3KYV A;  1VCX A;  2Z3R B;  1ZRP A;  4AI0 A;  1YK4 A;  1RWD A;  2M4V A;  2CKA A;  5DM7 1;  4AR6 A;  4K9F A;  3WWL A;  1RYQ A;  1YV1 A;  2ERJ A;  1DVB A;  4XGH A;  5EIN C;  2V3B B;  4AR4 A;  1R0J A;  3IU3 I;  1BRF A;  1RYT A;  4JAF A;  1T9O A;  4LHL A;  2J9U B;  1SMM A;  2LCQ A;  1BQ8 A;  2CR8 A;  1NXE A;  4AI3 A;  1VZG A;  1RDG A;  4POG A;  1S24 A; 
...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...