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


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