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 |
46
|
sequence length |
158
|
structure length |
158
|
Chain Sequence |
KIRIGHGFDVHKFGEPRPLILCGVEVPYETGLVAHSDGDVVLHAISDAILGAMALGDIGKHFPDTDAAYKGADSRVLLRHCYALAKAKGFELGNLDVTIIAQAPKMAPHIEDMRQVLAADLNADVADINVKATTTEKLGFTGRKEGIAVEAVVLLSRQ
|
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.
After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.
| publication title |
Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Shewanella oneidensis at 1.6 A: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity.
pubmed doi rcsb |
| molecule keywords |
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
|
| source organism |
Shewanella oneidensis
|
| molecule tags |
Lyase
|
| total genus |
46
|
| structure length |
158
|
| sequence length |
158
|
| chains with identical sequence |
B, C
|
| ec nomenclature |
ec
4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. |
| pdb deposition date | 2004-04-08 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF02542 | YgbB | YgbB family |
Image from the rcsb pdb (www.rcsb.org)
cath code
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Alpha Beta | 2-Layer Sandwich | 60s Ribosomal Protein L30; Chain: A; | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
#chains in the Genus database with same CATH superfamily 1IV3 A; 3F6M A; 1U43 A; 3FBA A; 3GHZ A; 3F0D A; 1JY8 A; 3K2X A; 1W57 A; 3K14 A; 1U3P A; 1IV4 A; 1U40 A; 3EOR A; 3IEQ A; 4C8E A; 4C8G A; 4C81 A; 3JVH A; 5B8F A; 1JN1 A; 2AMT A; 1KNK A; 3IKF A; 1U3L A; 2GZL A; 1YQN A; 4C82 A; 3P0Z A; 3Q8H A; 3P10 A; 3RE3 A; 3T80 A; 3F0E A; 3F0F A; 1W55 A; 1GX1 A; 1IV1 A; 3FPI A; 3QHD A; 1T0A A; 1KNJ A; 1IV2 A; 3MBM A; 2UZH A; 3IKE A; 3ELC A; 3ERN A; 3KE1 A; 3ESJ A; 4C8I A; 1H47 A; 1VH8 A; 3F0G A; 3IEW A; 3B6N A; 2PMP A; 1H48 A; 1VHA A; #chains in the Genus database with same CATH topology 4I50 B; 3RYH A; 1YJW F; 4TV8 A; 4BVT A; 1K8A H; 4G4W A; 1NQ3 A; 3RYC A; 4BY9 D; 4X3L A; 2ALE A; 5BMV B; 3N4Y A; 1OFU A; 4HNA A; 3S0H A; 3S06 A; 3Q8H A; 3T80 A; 3N2G B; 4RHA A; 3F0F A; 4BT2 A; 5IT9 M; 2CW4 A; 1COM A; 5EB1 B; 2HP3 A; 4X1I A; 5LYJ A; 1JFF B; 5JVD A; 3K2X A; 1XBI A; 1U40 A; 3JAK A; 1Q82 H; 3JAS A; 3LWR C; 2BTQ B; 1W5A A; 3N2K B; 5G4U C; 4ZHV A; 4BT6 A; 4X1K B; 3KIZ A; 5C8Y A; 3J7A R; 3CMA F; 1QD9 A; 1DT9 A; 2LBT A; 4NQ3 A; 3M1X A; 3FFM A; 3KHN A; 1GO0 A; 5CA0 A; 3BYQ A; 3LWO C; 2Q1X A; 2PMP A; 4X1Y B; 4O2A B; 4F6R B; 2Z01 A; 3AGK A; 4O4L A; 3CCE F; 2Z1F A; 2RHL A; 3M84 A; 3CC7 F; 3OBY A; 4TV9 B; 2RHJ A; 3CPQ A; 2ZOD A; 1RQ2 A; 2P6Y A; 3RYI A; 4O4J A; 5J2T A; 4RQO A; 3CCQ F; 4ZI7 B; 1UI9 A; 2RHH A; 3OBW A; 5LP6 C; 4DRX A; 5EO3 A; 3VOB A; 4O4I A; 4ZHQ A; 2HS3 A; 3JAM M; 1SA0 B; 2B33 A; 4EB6 B; 2GLZ A; 2KTU A; 3U0O A; 1FFX A; 2LBX A; 3E20 B; 4WBN A; 2Q1Y A; 3D00 A; 3CCV F; 3CCJ F; 3GHZ A; 3VCZ A; 4G4Z A; 2N48 A; 3V3T A; 1UFY A; 4BVS A; 3LDT A; 3CYQ A; 2AIF A; 2G9I A; 3HKC B; 3JVH A; 3D01 A; 2ZOV A; 3LWV C; 4I50 A; 3OW2 F; 3E1Y A; 4EI8 A; 1IPA A; 4C82 A; 3JAR B; 3HTN A; 3GTZ A; 3P0Z A; 4E6E A; 2BTO A; 4KWE A; 4B62 A; 5BMV A; 3DDN A; 3ZP4 A; 4PWT A; 3S03 A; 4X20 B; 3ZP7 A; 3N2G A; 2HS0 A; 5J2U B; 3CCR F; 5GIP C; 3CC4 F; 3LFO A; 3KJJ A; 2KGW A; 5IYZ B; 2OHW A; 4LNU B; 3PLA C; 5ITZ B; 3J80 M; 1Q8R A; 2ZVY A; 1JFF A; 2RHO A; 5AVM A; 1Q86 H; 2CWJ A; 1YQN A; 2NMU A; 3PAF A; 3CME F; 1SZQ A; 3I56 F; 4WBN B; 1QU9 A; 1X7O A; 3N2K A; 3RA5 A; 4X1K A; 1VK3 A; 4I55 B; 3F0G A; 1W2B F; 3NK7 A; 2ZAU A; 4O4H B; 5LP6 B; 4TZZ A; 4C4W C; 3S02 A; 1R1M A; 3VO8 A; 1VQO F; 2CHS A; 2VXY A; 1W5F A; 3WPW A; 3IR9 A; 1GZ0 A; 3K12 A; 4O2A A; 4X1Y A; 4F6R A; 5GON B; 2H8E A; 1NJI H; 5IJ9 B; 4XCQ A; 1U3L A; 4G4V A; 4DXD A; 4TV9 A; 3CC2 F; 3SIU A; 3F0E A; 5JH7 B; 1VQ4 F; 5DCV A; 3FPI A; 3QHD A; 3HJW C; 2IAF A; 4ZI7 A; 1J7H A; 3VYS C; 1ODE A; 3HKD B; 2VAW A; 4EI9 A; 2UYN B; 3TD4 A; 1IV3 A; 2OTM A; 3FBA A; 1SA0 A; 4EB6 A; 3CD6 F; 4O2B B; 1JJ2 F; 5FNV B; 5CB4 B; 4YJ3 B; 3HKE B; 3HKB A; 3CCL F; 2AMT A; 3I3F A; 1KNK A; 1W40 A; 4U39 A; 5LXT B; 1GO1 A; 5KX5 B; 5LA6 B; 1VQ9 F; 4LCK A; 4U3J B; 2IG8 A; 3M4S A; 5HP7 A; 1IV1 A; 3WJQ A; 1KNJ A; 3HKC A; 3KJK A; 1YJN F; 3QTY A; 3JAR A; 4BVR A; 2Z1U A; 4ZK7 A; 2FGY A; 1YIJ F; 1W5E A; 3CCS F; 1W57 A; 3JAT B; 3G71 F; 4X20 A; 5CA1 B; 5GIN C; 1QVG F; 5J2U A; 5KMG B; 2DYY A; 3R0P A; 3MCA B; 5IYZ A; 2H8C A; 2GZL A; 3DC2 A; 4LNU A; 4I4T B; 3ZOP A; 3LWQ C; 5ITZ A; 2LCA A; 2PHN A; 1XRG A; 1ZWZ A; 2IQQ A; 3HWU A; 3WJR A; 5GIO C; 1VQ6 F; 1CN7 A; 1W59 A; 4BT4 A; 3NVK E; 1E7K A; 1X52 A; 3HKB B; 2GVI A; 5IJ0 B; 4I55 A; 2QI2 A; 3O85 A; 2I6R A; 4O4H A; 5LP6 A; 4EI7 A; 1CK2 A; 5MN4 A; 3TD5 A; 5HY1 A; 5HP8 A; 3WPX A; 2HVY D; 4BW0 B; 3IKE A; 5GON A; 3LWP C; 5IJ9 A; 5GAN K; 3ELC A; 2HP0 B; 3P4E A; 3TD3 A; 5A2Q M; 4YJ2 A; 3VTI C; 1RQ7 A; 3VOA A; 5HXU A; 5JH7 A; 1Q81 H; 4B45 A; 4M8I A; 1K73 H; 5FJ4 C; 1FSZ A; 3SIV A; 1VQL F; 1U3P A; 1W41 A; 1FNJ A; 3HKD A; 3D54 A; 2UYN A; 2JNB A; 2HS4 A; 4C81 A; 1N8R H; 4ERH A; 5EZY B; 1W5B A; 1K9M H; 2Z1E A; 3RE3 A; 4O2B A; 2LBW A; 5FNV A; 5CB4 A; 4YJ3 A; 1RA4 A; 3HKE A; 5LXT A; 2AIZ P; 5KX5 A; 5LA6 A; 2ZVZ A; 2OZB A; 3WJP A; 1Z5V A; 4U3J A; 3L7Q A; 1TUB B; 2CZW A; 5JCO C; 3S0W A; 3VYT C; 2KG4 A; 1H48 A; 1VHA A; 3I7T A; 2BO1 A; 3NK6 A; 1TVK B; 3JAL B; 2R75 1; 4G4Y A; 3C8L A; 1H7M A; 1RLU A; 3GYQ A; 3QUW A; 2L26 A; 4YJ2 B; 4ZHY B; 3JAT A; 5CA1 A; 3V7E A; 4B46 A; 1W58 1; 5KMG A; 4ZHW A; 5LOV A; 2UYK A; 5HY4 A; 1KQS F; 2HRU A; 4I4T A; 2YYE A; 5EIB D; 1OAP A; 3F6M A; 2QTP A; 4IIJ B; 5JQG B; 4G88 A; 3IEQ A; 4IHJ B; 1M90 H; 1VQ7 F; 4C8E A; 3CCM F; 3CPW F; 3ZO8 A; 3IKF A; 2QA4 F; 5HWE A; 1QVF F; 5IJ0 A; 3UT5 B; 1DBF A; 1W42 A; 3N4Z A; 5G4V C; 4BT7 A; 2I6D A; 3HAX D; 1CLI A; 2HRY A; 1SDS A; 3JCM M; 3WGN A; 3C9S A; 3NMU C; 1KD1 H; 4C8I A; 4FFB B; 3MDO A; 3E22 B; 5FLX M; 2QEX F; 3FD6 A; 2VAP A; 1PF5 A; 2VAM A; 3V7Q A; 2HP0 A; 5HY0 A; 2VGN A; 3RYF B; 3VI6 A; 3FD5 A; 5EYP B; 1FNK A; 2MQE A; 2RB9 A; 3OON A; 5GAP K; 1ONI A; 5LOV B; 3MCQ A; 3V4D A; 2R6R 1; 4TUY B; 2ZF8 A; 3CYP B; 1T0K B; 3P10 A; 5MN5 A; 3RYH B; 3C9T A; 4NWO B; 4TV8 B; 5EAZ A; 2V9Y A; 3WGK A; 5EZY A; 1S72 F; 3LYB A; 3RYC B; 3C9R A; 3RA6 A; 3VMF B; 3G6E F; 3JAW A; 3CXC F; 3C9U A; 1JY8 A; 3CG6 A; 4HNA B; 5EWR A; 1X25 A; 3EOR A; 1TUB A; 4C8G A; 2EWC A; 3S0Y A; 2F9Z C; 1X7P A; 1QAH A; 2CSL A; 1VQV A; 3VYU C; 1M1K H; 2W8B C; 1TVK A; 3JAL A; 4X1I B; 2UYP A; 4BT3 A; 5LYJ B; 2OTJ F; 2BTU A; 5JVD B; 1IV2 A; 3WGM A; 3LME A; 2HQS C; 3JAK B; 2WAL A; 3NVI B; 3JAS B; 4R40 B; 1H47 A; 1VH8 A; 2CHT A; 4ZOL A; 3CB2 A; 4BVQ A; 3ERN A; 1NMU B; 1VQM F; 1VQ5 F; 1U43 A; 3F0D A; 3K14 A; 2DT4 A; 5C8Y B; 1Z5W A; 2OTL F; 4X3M A; 1JN1 A; 4IIJ A; 5JQG A; 2VGM A; 3I55 F; 3J81 M; 5CA0 B; 2KTV A; 3G4S F; 2CVL A; 4IHJ A; 1W55 A; 4O4L B; 3JAW B; 3MBM A; 5EIB C; 3WXM B; 1YGY A; 2HX0 A; 3ESJ A; 3UT5 A; 1YIT F; 3B6N A; 4BT5 A; 3RYI B; 4O4J B; 5J2T B; 3ON1 A; 1VQK F; 1IV4 A; 1Q7Y H; 4B5C A; 4NUT A; 3K0T A; 2FC3 A; 4DRX B; 5HXZ A; 4O4I B; 4FFB A; 4ZHQ B; 3E22 A; 2Z1T A; 3WGL A; 5HY2 A; 5MN6 A; 1YHQ F; 1XV2 A; 2K1S A; 5B8F A; 3VIU A; 1YI2 F; 1VQP F; 3MQW A; 1FFX B; 1KC8 H; 1JD1 A; 3RYF A; 3WGJ A; 1YJ9 F; 1VQ8 F; 5EYP A; 1GX1 A; 2H6L A; 4ZOL B; 1T0A A; 5JCO A; 1W3E X; 2UZH A; 3KE1 A; 1RLG A; 5EB0 A; 4TUY A; 3CCU F; 2UYJ A; 3IEW A; 3IMP A; 2YXZ A; 1PXW A; 4G4X A; 1XHO A; 1VQN F; #chains in the Genus database with same CATH homology 1IV3 A; 3F6M A; 1U43 A; 3FBA A; 3GHZ A; 3F0D A; 1JY8 A; 3K2X A; 1W57 A; 3K14 A; 1U3P A; 1IV4 A; 1U40 A; 3EOR A; 3IEQ A; 4C8E A; 4C8G A; 4C81 A; 3JVH A; 5B8F A; 1JN1 A; 2AMT A; 1KNK A; 3IKF A; 1U3L A; 2GZL A; 1YQN A; 4C82 A; 3P0Z A; 3Q8H A; 3P10 A; 3RE3 A; 3T80 A; 3F0E A; 3F0F A; 1W55 A; 1GX1 A; 1IV1 A; 3FPI A; 3QHD A; 1T0A A; 1KNJ A; 1IV2 A; 3MBM A; 2UZH A; 3IKE A; 3ELC A; 3ERN A; 3KE1 A; 3ESJ A; 4C8I A; 1H47 A; 1VH8 A; 3F0G A; 3IEW A; 3B6N A; 2PMP A; 1H48 A; 1VHA A;
#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...
