4JD7A

Crystal structure of pput_1285, a putative hydroxyproline epimerase from pseudomonas putida f1 (target efi-506500), open form, space group p212121, bound sulfate
Total Genus 79
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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
79
sequence length
314
structure length
314
Chain Sequence
NLYFQSMKQIHVIDSHTGGEPTRLVMKGFPQLHGRSMAEQRDELRELHDRWRRACLLEPRGNDVLVGALYCPPVSADATCGVIFFNNAGYLNMCGHGTIGLVASLQHLGLIAPGVHKIDTPVGQVSATLHEDGAITVANVPSYRYRQHVAVNVPGHGVVHGDIAWGGNWFFLVAEHGQRIELDNREVLTEYTWAMLKALEAQGITGENGAPIDHVELFADDPNADSRNFVMCPGKAYDRSPCGTGTSAKLACLAADGTLAEGQTWVQASITGSQFHGRYERDGERIRPFITGRAHMTADSTLLIDEQDPFAWGI
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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 P212121, bound sulfate
rcsb
source organism Pseudomonas putida
molecule tags Isomerase
molecule keywords Proline racemase
total genus 79
structure length 314
sequence length 314
chains with identical sequence D
ec nomenclature ec 5.1.1.8: 4-hydroxyproline epimerase.
pdb deposition date 2013-02-24

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 4jd7A02
3.10.310.10 Alpha Beta Roll Diaminopimelate Epimerase; Chain A, domain 1 Diaminopimelate Epimerase; Chain A, domain 1 4jd7A01
1U0KA 1SDJA 4J9WA 4K8LA 4LB0A 5HA4A 1QYAA 1QY9A 4Q60A 2PW0A 4JD7A 4K7GB 1U1VA 1U1XA 5IWEA 1W62A 2Q9JA 1T6KA 5M47A 1BWZA 1XUAA 2GKJA 1TM0A 1S7JA 2GKEA 4J9XA 3G7KA 3EDNA 1YM5A 1XUBA 1W61A 1GQZA 4K7XA 2AZPA 3EKMA 4IJZA 4JBDA 2H9FA 4Q2HA 5H2YA 4DUNA 5H2GA 2PVZA 3FVEA 3EJXA 4JUUA 2Q9HA 4JCIA 1U1WA 2OTNA 4IK0A
chains in the Genus database with same CATH superfamily
1U0KA 2MPBA 4J9WA 5HA4A 4PY9A 4Q60A 4LG3A 3ICJA 5M47A 3WQZA 1WPPA 4J9XA 2LT2A 1YM5A 4JBDA 4DUNA 1K23A 4GL6A 3DEVA 2Q9HA 2ZXOA 2OTNA 2YMAA 1SDJA 4K8LA 4OA3A 4LB0A 3IGHX 2PW0A 1U1VA 1W62A 2Q9JA 1T6KA 2GKJA 2KPTA 1S7JA 2GKEA 2HAWA 3G7KA 2ENXA 4K7XA 2AZPA 4IJZA 4Q2HA 2H9FA 5H2YA 4LS9A 5H2GA 3FVEA 4JUUA 2ZXRA 2EB0A 2IW4A 4JD7A 4RPAA 1U1XA 1BWZA 1TM0A 3PVHA 2QB6A 3PW9A 3EDNA 2ZXPA 1W61A 1GQZA 2QB8A 1I74A 2PVZA 1K20A 1WPMA 1IR6A 5ANPA 3W5WA 2KW7A 1QYAA 1QY9A 4K7GB 5IWEA 2QB7A 1XUAA 3PTJA 1XUBA 3G98A 3EKMA 2ZVFA 3EJXA 4JCIA 1U1WA 4IK0A
chains in the Genus database with same CATH topology
1U0KA 2MPBA 4J9WA 5HA4A 4PY9A 4Q60A 4LG3A 3ICJA 5M47A 3WQZA 1WPPA 4J9XA 2LT2A 1YM5A 4JBDA 4DUNA 1K23A 4GL6A 3DEVA 2Q9HA 2ZXOA 2OTNA 2YMAA 1SDJA 4K8LA 4OA3A 4LB0A 3IGHX 2PW0A 1U1VA 1W62A 2Q9JA 1T6KA 2GKJA 2KPTA 1S7JA 2GKEA 2HAWA 3G7KA 2ENXA 4K7XA 2AZPA 4IJZA 4Q2HA 2H9FA 5H2YA 4LS9A 5H2GA 3FVEA 4JUUA 2ZXRA 2EB0A 2IW4A 4JD7A 4RPAA 1U1XA 1BWZA 1TM0A 3PVHA 2QB6A 3PW9A 3EDNA 2ZXPA 1W61A 1GQZA 2QB8A 1I74A 2PVZA 1K20A 1WPMA 1IR6A 5ANPA 3W5WA 2KW7A 1QYAA 1QY9A 4K7GB 5IWEA 2QB7A 1XUAA 3PTJA 1XUBA 3G98A 3EKMA 2ZVFA 3EJXA 4JCIA 1U1WA 4IK0A
chains in the Genus database with same CATH homology


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