4JBDA

Crystal structure of pput_1285, a putative hydroxyproline epimerase from pseudomonas putida f1 (target efi-506500), open form, space group i2, bound citrate
Total Genus 85
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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
85
sequence length
308
structure length
308
Chain Sequence
MKQIHVIDSHTGGEPTRLVMKGFPQLHGRSMAEQRDELRELHDRWRRACLLEPRGNDVLVGALYCPPVSADATCGVIFFNNAGYLNMCGHGTIGLVASLQHLGLIAPGVHKIDTPVGQVSATLHEDGAITVANVPSYRYRQHVAVNVPGHGVVHGDIAWGGNWFFLVAEHGQRIELDNREVLTEYTWAMLKALEAQGITGENGAPIDHVELFADDPNADSRNFVMCPGKAYDRSPCGTGTSAKLACLAADGTLAEGQTWVQASITGSQFHGRYERDGERIRPFITGRAHMTADSTLLIDEQDPFAWGI
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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.

Chord Diagram
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publication title Crystal structure of pput_1285, a putative hydroxyproline epimerase from pseudomonas putida f1 (target efi-506500), open form, space group i2, bound citrate
rcsb
source organism Pseudomonas putida
molecule tags Isomerase
molecule keywords Proline racemase
total genus 85
structure length 308
sequence length 308
ec nomenclature ec 5.1.1.8: 4-hydroxyproline epimerase.
pdb deposition date 2013-02-19

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF05544 Pro_racemase Proline racemase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 4jbdA02
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 4jbdA01
3G7KA 2OTNA 3EDNA 4K7GB 4K7XA 4IJZA 1T6KA 5M47A 2GKJA 4LB0A 4Q2HA 1U0KA 1U1XA 4JCIA 1S7JA 1U1WA 4K8LA 5IWEA 1GQZA 4JBDA 3EJXA 5H2YA 4DUNA 3EKMA 4JUUA 1U1VA 1TM0A 1QYAA 4Q60A 2AZPA 1YM5A 1BWZA 1W61A 2H9FA 1SDJA 1XUAA 5H2GA 2Q9HA 4J9WA 1W62A 1QY9A 4J9XA 5HA4A 2PW0A 2GKEA 2PVZA 4IK0A 4JD7A 1XUBA 2Q9JA 3FVEA
chains in the Genus database with same CATH superfamily
3IGHX 3EDNA 3DEVA 2ZXPA 2QB6A 1U1XA 2YMAA 4K8LA 1GQZA 2HAWA 3EJXA 4DUNA 3EKMA 1U1VA 4Q60A 1YM5A 3WQZA 1XUAA 1QY9A 3PTJA 3G98A 3ICJA 1XUBA 3G7KA 4K7XA 1T6KA 1S7JA 4PY9A 4LG3A 3PVHA 4JBDA 1WPPA 4JUUA 1TM0A 4RPAA 1BWZA 1W61A 1W62A 2GKEA 2KW7A 4IK0A 4Q2HA 2ZVFA 5IWEA 2ZXOA 2QB8A 4GL6A 5M47A 4LS9A 2GKJA 2ZXRA 1U0KA 4JCIA 1U1WA 4OA3A 5ANPA 1I74A 1QYAA 2AZPA 3W5WA 2H9FA 1SDJA 2Q9HA 4J9WA 4J9XA 4JD7A 2IW4A 3PW9A 2Q9JA 1IR6A 2OTNA 2ENXA 4K7GB 4IJZA 2MPBA 4LB0A 2QB7A 2EB0A 5H2YA 1K23A 5H2GA 2KPTA 5HA4A 2PW0A 2PVZA 1K20A 2LT2A 1WPMA 3FVEA
chains in the Genus database with same CATH topology
3IGHX 3EDNA 3DEVA 2ZXPA 2QB6A 1U1XA 2YMAA 4K8LA 1GQZA 2HAWA 3EJXA 4DUNA 3EKMA 1U1VA 4Q60A 1YM5A 3WQZA 1XUAA 1QY9A 3PTJA 3G98A 3ICJA 1XUBA 3G7KA 4K7XA 1T6KA 1S7JA 4PY9A 4LG3A 3PVHA 4JBDA 1WPPA 4JUUA 1TM0A 4RPAA 1BWZA 1W61A 1W62A 2GKEA 2KW7A 4IK0A 4Q2HA 2ZVFA 5IWEA 2ZXOA 2QB8A 4GL6A 5M47A 4LS9A 2GKJA 2ZXRA 1U0KA 4JCIA 1U1WA 4OA3A 5ANPA 1I74A 1QYAA 2AZPA 3W5WA 2H9FA 1SDJA 2Q9HA 4J9WA 4J9XA 4JD7A 2IW4A 3PW9A 2Q9JA 1IR6A 2OTNA 2ENXA 4K7GB 4IJZA 2MPBA 4LB0A 2QB7A 2EB0A 5H2YA 1K23A 5H2GA 2KPTA 5HA4A 2PW0A 2PVZA 1K20A 2LT2A 1WPMA 3FVEA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3G7K A;  2OTN A;  3EDN A;  4K7G B;  4K7X A;  4IJZ A;  1T6K A;  5M47 A;  2GKJ A;  4LB0 A;  4Q2H A;  1U0K A;  1U1X A;  4JCI A;  1S7J A;  1U1W A;  4K8L A;  5IWE A;  1GQZ A;  4JBD A;  3EJX A;  5H2Y A;  4DUN A;  3EKM A;  4JUU A;  1U1V A;  1TM0 A;  1QYA A;  4Q60 A;  2AZP A;  1YM5 A;  1BWZ A;  1W61 A;  2H9F A;  1SDJ A;  1XUA A;  5H2G A;  2Q9H A;  4J9W A;  1W62 A;  1QY9 A;  4J9X A;  5HA4 A;  2PW0 A;  2GKE A;  2PVZ A;  4IK0 A;  4JD7 A;  1XUB A;  2Q9J A;  3FVE A; 
#chains in the Genus database with same CATH topology
 3IGH X;  3EDN A;  3DEV A;  2ZXP A;  2QB6 A;  1U1X A;  2YMA A;  4K8L A;  1GQZ A;  2HAW A;  3EJX A;  4DUN A;  3EKM A;  1U1V A;  4Q60 A;  1YM5 A;  3WQZ A;  1XUA A;  1QY9 A;  3PTJ A;  3G98 A;  3ICJ A;  1XUB A;  3G7K A;  4K7X A;  1T6K A;  1S7J A;  4PY9 A;  4LG3 A;  3PVH A;  4JBD A;  1WPP A;  4JUU A;  1TM0 A;  4RPA A;  1BWZ A;  1W61 A;  1W62 A;  2GKE A;  2KW7 A;  4IK0 A;  4Q2H A;  2ZVF A;  5IWE A;  2ZXO A;  2QB8 A;  4GL6 A;  5M47 A;  4LS9 A;  2GKJ A;  2ZXR A;  1U0K A;  4JCI A;  1U1W A;  4OA3 A;  5ANP A;  1I74 A;  1QYA A;  2AZP A;  3W5W A;  2H9F A;  1SDJ A;  2Q9H A;  4J9W A;  4J9X A;  4JD7 A;  2IW4 A;  3PW9 A;  2Q9J A;  1IR6 A;  2OTN A;  2ENX A;  4K7G B;  4IJZ A;  2MPB A;  4LB0 A;  2QB7 A;  2EB0 A;  5H2Y A;  1K23 A;  5H2G A;  2KPT A;  5HA4 A;  2PW0 A;  2PVZ A;  1K20 A;  2LT2 A;  1WPM A;  3FVE A; 
#chains in the Genus database with same CATH homology
 3IGH X;  3EDN A;  3DEV A;  2ZXP A;  2QB6 A;  1U1X A;  2YMA A;  4K8L A;  1GQZ A;  2HAW A;  3EJX A;  4DUN A;  3EKM A;  1U1V A;  4Q60 A;  1YM5 A;  3WQZ A;  1XUA A;  1QY9 A;  3PTJ A;  3G98 A;  3ICJ A;  1XUB A;  3G7K A;  4K7X A;  1T6K A;  1S7J A;  4PY9 A;  4LG3 A;  3PVH A;  4JBD A;  1WPP A;  4JUU A;  1TM0 A;  4RPA A;  1BWZ A;  1W61 A;  1W62 A;  2GKE A;  2KW7 A;  4IK0 A;  4Q2H A;  2ZVF A;  5IWE A;  2ZXO A;  2QB8 A;  4GL6 A;  5M47 A;  4LS9 A;  2GKJ A;  2ZXR A;  1U0K A;  4JCI A;  1U1W A;  4OA3 A;  5ANP A;  1I74 A;  1QYA A;  2AZP A;  3W5W A;  2H9F A;  1SDJ A;  2Q9H A;  4J9W A;  4J9X A;  4JD7 A;  2IW4 A;  3PW9 A;  2Q9J A;  1IR6 A;  2OTN A;  2ENX A;  4K7G B;  4IJZ A;  2MPB A;  4LB0 A;  2QB7 A;  2EB0 A;  5H2Y A;  1K23 A;  5H2G A;  2KPT A;  5HA4 A;  2PW0 A;  2PVZ A;  1K20 A;  2LT2 A;  1WPM A;  3FVE 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)

 
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#similar chains, but unknotted
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