SMTL ID : 3lub.2 (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.1 ZN.6: 5 residues within 4Å: Chain B: E.32, D.43, H.120, H.163 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.32, B:D.43, B:H.120, H2O.9, H2O.12 ZN.7: 5 residues within 4Å: Chain B: H.34, D.43, H.163, E.168 Ligands: ZN.6 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.8 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.18, H2O.18 ZN.10: 5 residues within 4Å: Chain C: H.34, D.43, H.163, 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.18 ZN.14: 5 residues within 4Å: Chain D: E.32, D.43, H.120, H.163 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.32, D:D.43, D:H.120, H2O.25, H2O.27 ZN.15: 5 residues within 4Å: Chain D: H.34, D.43, H.163, E.168 Ligands: ZN.14 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.25 ZN.19: 6 residues within 4Å: Chain E: E.32, H.34, D.43, H.120, H.163 Ligands: ZN.20 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.32, E:D.43, E:H.120, H2O.32, H2O.32 ZN.20: 5 residues within 4Å: Chain E: H.34, D.43, H.163, E.168 Ligands: ZN.19 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.32 ZN.24: 5 residues within 4Å: Chain F: E.32, D.43, H.120, H.163 Ligands: ZN.25 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.32, F:D.43, F:H.120, H2O.37, H2O.40 ZN.25: 5 residues within 4Å: Chain F: H.34, D.43, H.163, E.168 Ligands: ZN.24 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.37

5 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: 1 residues within 4Å: Chain C: D.210 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.210, H2O.18, H2O.19, H2O.20, H2O.21 CA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.4: 6 residues within 4Å: Chain A: L.26, M.69, P.70 Chain B: T.31, P.73, F.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.31 EDO.17: 7 residues within 4Å: Chain C: T.31, P.73, F.74 Chain D: L.26, M.69, P.70, I.102 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.31, C:T.31 EDO.21: 6 residues within 4Å: Chain E: L.26, M.69, P.70 Chain F: T.31, P.73, F.74 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.31, F:T.31 EDO.22: 6 residues within 4Å: Chain D: F.134 Chain E: G.80, Q.81, R.82, E.83 Chain F: V.108 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.80, E:G.80, E:R.82, E:R.82, E:R.82, E:E.83, E:E.83 EDO.27: 7 residues within 4Å: Chain E: T.31, P.73, F.74, I.88 Chain F: L.26, M.69, P.70 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:T.31, F:P.70

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

CL.5: 3 residues within 4Å: Chain A: N.78, P.206, R.207 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: N.78, P.206, R.207 Chain C: R.130 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: N.78, P.206, R.207 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain D: N.78, P.206, R.207 Chain E: R.130 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain E: N.78, R.207 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain F: N.78, R.207 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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
G

B
H

C
I

D
J

E
K

F
L

Putative creatinine amidohydrolase

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