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
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
85
sequence length
308
structure length
308
Chain Sequence
MKQIHVIDSHTGGEPTRLVMKGFPQLHGRSMAEQRDELRELHDRWRRACLLEPRGNDVLVGALYCPPVSADATCGVIFFNNAGYLNMCGHGTIGLVASLQHLGLIAPGVHKIDTPVGQVSATLHEDGAITVANVPSYRYRQHVAVNVPGHGVVHGDIAWGGNWFFLVAEHGQRIELDNREVLTEYTWAMLKALEAQGITGENGAPIDHVELFADDPNADSRNFVMCPGKAYDRSPCGTGTSAKLACLAADGTLAEGQTWVQASITGSQFHGRYERDGERIRPFITGRAHMTADSTLLIDEQDPFAWGI
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 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
3EJXA 1XUBA 2PW0A 2GKEA 1YM5A 1GQZA 1U0KA 4J9XA 1TM0A 2Q9HA 1T6KA 1W61A 3EKMA 1QYAA 1U1XA 4IJZA 2AZPA 4K7GB 5H2YA 4Q2HA 4JD7A 3G7KA 1BWZA 5H2GA 1W62A 4JUUA 4DUNA 1S7JA 2PVZA 4JCIA 2OTNA 1U1VA 2Q9JA 5M47A 3EDNA 2H9FA 1SDJA 5IWEA 1XUAA 4JBDA 2GKJA 1U1WA 4J9WA 1QY9A 4K8LA 4IK0A 4Q60A 5HA4A 4LB0A 4K7XA 3FVEA
chains in the Genus database with same CATH superfamily
3EJXA 2GKEA 1U0KA 2Q9HA 3EKMA 1IR6A 4IJZA 1U1XA 2AZPA 3G7KA 4JUUA 4DUNA 1U1WA 4IK0A 2LT2A 4Q60A 4LB0A 4K7XA 2QB6A 1XUBA 1K23A 4J9XA 2MPBA 5H2YA 4Q2HA 4JD7A 3W5WA 2EB0A 5H2GA 2PVZA 2Q9JA 2QB7A 4LG3A 2YMAA 3G98A 1QY9A 3PW9A 2ZXOA 2ENXA 2PW0A 1K20A 1GQZA 2QB8A 1QYAA 2ZVFA 1BWZA 1S7JA 1I74A 3WQZA 3ICJA 4GL6A 5M47A 3EDNA 2H9FA 1SDJA 1XUAA 2ZXPA 4JBDA 2GKJA 4K8LA 5HA4A 3PVHA 3DEVA 4OA3A 2KPTA 3FVEA 1YM5A 1WPMA 1TM0A 1T6KA 1W61A 4K7GB 3IGHX 2ZXRA 1W62A 2KW7A 4RPAA 4JCIA 2OTNA 1U1VA 1WPPA 5ANPA 2HAWA 2IW4A 5IWEA 4LS9A 4J9WA 4PY9A 3PTJA
chains in the Genus database with same CATH topology
3EJXA 2GKEA 1U0KA 2Q9HA 3EKMA 1IR6A 4IJZA 1U1XA 2AZPA 3G7KA 4JUUA 4DUNA 1U1WA 4IK0A 2LT2A 4Q60A 4LB0A 4K7XA 2QB6A 1XUBA 1K23A 4J9XA 2MPBA 5H2YA 4Q2HA 4JD7A 3W5WA 2EB0A 5H2GA 2PVZA 2Q9JA 2QB7A 4LG3A 2YMAA 3G98A 1QY9A 3PW9A 2ZXOA 2ENXA 2PW0A 1K20A 1GQZA 2QB8A 1QYAA 2ZVFA 1BWZA 1S7JA 1I74A 3WQZA 3ICJA 4GL6A 5M47A 3EDNA 2H9FA 1SDJA 1XUAA 2ZXPA 4JBDA 2GKJA 4K8LA 5HA4A 3PVHA 3DEVA 4OA3A 2KPTA 3FVEA 1YM5A 1WPMA 1TM0A 1T6KA 1W61A 4K7GB 3IGHX 2ZXRA 1W62A 2KW7A 4RPAA 4JCIA 2OTNA 1U1VA 1WPPA 5ANPA 2HAWA 2IW4A 5IWEA 4LS9A 4J9WA 4PY9A 3PTJA
chains in the Genus database with same CATH homology


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