SMTL ID : 3lub.1 (1 other biounit)

Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: E.32, D.43, H.120, H.163 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.32, A:D.43, A:H.120, H2O.1, H2O.2 ZN.2: 6 residues within 4Å: Chain A: H.34, T.42, D.43, H.163, E.168 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.34, A:D.43, A:E.168, A:E.168, H2O.2 ZN.5: 5 residues within 4Å: Chain B: E.32, D.43, H.120, H.163 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.32, B:D.43, B:H.120, H2O.7, H2O.10 ZN.6: 5 residues within 4Å: Chain B: H.34, D.43, H.163, E.168 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.34, B:D.43, B:E.168, B:E.168, H2O.7 ZN.9: 5 residues within 4Å: Chain C: E.32, D.43, H.120, H.163 Ligands: ZN.10 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.32, C:D.43, C:H.120, H2O.14, H2O.14 ZN.10: 5 residues within 4Å: Chain C: H.34, D.43, G.119, E.168 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.34, C:D.43, C:E.168, C:E.168, H2O.14 ZN.15: 6 residues within 4Å: Chain D: E.32, H.34, D.43, H.120, H.163 Ligands: ZN.16 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.32, D:D.43, D:H.120, H2O.22, H2O.22 ZN.16: 5 residues within 4Å: Chain D: H.34, D.43, H.163, E.168 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.34, D:D.43, D:E.168, D:E.168, H2O.21 ZN.22: 6 residues within 4Å: Chain E: E.32, H.34, D.43, H.120, H.163 Ligands: ZN.23 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.32, E:D.43, E:H.120, H2O.30, H2O.33 ZN.23: 5 residues within 4Å: Chain E: H.34, D.43, H.163, E.168 Ligands: ZN.22 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.34, E:D.43, E:E.168, E:E.168, H2O.30 ZN.29: 5 residues within 4Å: Chain F: E.32, D.43, H.120, H.163 Ligands: ZN.30 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.32, F:D.43, F:H.120, H2O.38, H2O.41 ZN.30: 5 residues within 4Å: Chain F: H.34, D.43, H.163, E.168 Ligands: ZN.29 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.34, F:D.43, F:E.168, F:E.168, H2O.38

7 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.17: 1 residues within 4Å: Chain D: D.210 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.210, H2O.25, H2O.25, H2O.25, H2O.27 CA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.24: 1 residues within 4Å: Chain E: D.210 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.210, H2O.32, H2O.33, H2O.34, H2O.36 CA.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: N.78, P.206, R.207 Chain F: R.130 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: N.78, P.206, R.207 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: N.78, P.206, R.207 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain D: N.78, P.206, R.207 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain E: G.80, Q.81, R.82, E.83 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain E: N.78, P.206, R.207 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain A: R.130 Chain F: N.78, P.206, R.207 Ligand excluded by PLIP

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 7 residues within 4Å: Chain A: T.31, P.73, F.74 Chain B: L.26, M.69, P.70, I.102 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.70, A:T.31 EDO.12: 6 residues within 4Å: Chain B: F.134 Chain C: G.80, Q.81, R.82, E.83 Chain D: V.108 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.80, C:G.80, C:R.82, C:R.82, C:R.82, C:E.83 EDO.13: 6 residues within 4Å: Chain C: L.26, M.69, P.70 Chain D: T.31, P.73, F.74 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.31 EDO.19: 4 residues within 4Å: Chain D: S.104, H.107, V.108, Y.136 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.104, D:H.107 Water bridges: C:R.82 EDO.20: 5 residues within 4Å: Chain C: V.108 Chain D: G.80, Q.81, R.82, E.83 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.80, D:R.82, D:R.82, D:E.83, D:E.83 EDO.26: 7 residues within 4Å: Chain E: L.26, M.69, P.70, V.72 Chain F: T.31, P.73, F.74 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:T.31, F:T.31, E:P.70

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution. To be published

Release Date

2010-03-09

Peptides

Putative creatinine amidohydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Putative creatinine amidohydrolase

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