SMTL ID : 3no4.1

Crystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC 73102 at 2.00 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.50, D.59, E.191 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.50, A:D.59, A:E.191, H2O.4, H2O.8 NI.7: 3 residues within 4Å: Chain B: H.50, D.59, E.191 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.50, B:D.59, B:E.191, H2O.12, H2O.12 NI.17: 3 residues within 4Å: Chain C: H.50, D.59, E.191 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.50, C:D.59, C:E.191, H2O.20, H2O.20 NI.24: 3 residues within 4Å: Chain D: H.50, D.59, E.191 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.50, D:D.59, D:E.191, H2O.27, H2O.31 NI.30: 3 residues within 4Å: Chain E: H.50, D.59, E.191 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.50, E:D.59, E:E.191, H2O.35, H2O.35 NI.40: 3 residues within 4Å: Chain F: H.50, D.59, E.191 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.50, F:D.59, F:E.191, H2O.42, H2O.42

6 x UNL: UNKNOWN LIGAND

UNL.2: 5 residues within 4Å: Chain A: E.48, H.89, H.90, H.129, H.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.89, A:G.131 Water bridges: A:E.48, A:H.129 UNL.8: 7 residues within 4Å: Chain B: H.89, H.90, H.129, G.130, G.131, S.185, H.186 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.129, B:H.129, B:G.130, B:G.131, B:H.186 Water bridges: B:H.129 UNL.18: 5 residues within 4Å: Chain C: H.89, H.90, H.129, G.131, H.186 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.89, C:H.89, C:H.129, C:G.131, C:H.186 Water bridges: C:E.48, C:G.130 UNL.25: 5 residues within 4Å: Chain D: E.48, H.89, H.90, H.129, H.186 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.90, D:G.131, D:H.186 UNL.31: 7 residues within 4Å: Chain E: H.89, H.90, H.129, G.130, G.131, S.185, H.186 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:H.129, E:G.130, E:G.131, E:H.186, E:H.186 Water bridges: E:H.186 UNL.41: 5 residues within 4Å: Chain F: H.89, H.90, H.129, G.131, H.186 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:H.90, F:G.131, F:H.186 Water bridges: F:E.48, F:D.59, F:G.130, F:G.130

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

CL.3: 1 residues within 4Å: Ligands: CL.26 Ligand excluded by PLIP CL.26: 1 residues within 4Å: Ligands: CL.3 Ligand excluded by PLIP

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

EDO.4: 5 residues within 4Å: Chain A: D.110, T.113, C.114 Chain B: L.88 Chain C: A.145 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: Q.161, F.263, A.266 Chain D: R.217, Y.219 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: A.145 Chain D: L.88, R.100 Chain E: D.110, T.113, C.114 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain B: G.19, M.20, L.21, A.68, G.71, D.72, V.78 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain B: A.163, N.164, M.167, C.168 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain B: D.149, L.150, Q.151 Chain D: D.149, L.150, Q.151 Chain F: D.149, L.150, Q.151 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: K.137, Q.161, V.162 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: L.34, Q.35, K.38, A.118, G.119 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: Q.161, F.263 Chain C: R.217, Y.219 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain B: A.73, K.254 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: K.117, L.150, Q.151 Chain D: Q.151 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: A.145 Chain C: L.88 Chain F: D.110, T.113, C.114 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain C: Q.161, V.162 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain C: K.117, A.118 Chain F: T.91, A.92, F.93, P.94 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain C: G.19, M.20, L.21, A.68, G.71, D.72, V.78 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: A.163, N.164, M.167, C.168 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain D: D.110, T.113, C.114 Chain E: L.88 Chain F: A.145 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: R.217, Y.219 Chain D: Q.161, F.263, A.266 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: L.88, R.100 Chain B: D.110, T.113, C.114 Chain D: A.145 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain E: G.19, M.20, L.21, A.68, G.71, D.72, V.78 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain E: A.163, N.164, M.167, C.168 Ligand excluded by PLIP EDO.34: 9 residues within 4Å: Chain A: D.149, L.150, Q.151 Chain C: D.149, L.150, Q.151 Chain E: D.149, L.150, Q.151 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain E: K.137, Q.161, V.162 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain E: L.34, Q.35, K.38, A.118, G.119 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain E: Q.161, F.263 Chain F: R.217, Y.219 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain E: A.73, K.254 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain A: Q.151 Chain E: K.117, L.150, Q.151 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain C: D.110, T.113, C.114 Chain E: A.145 Chain F: L.88 Ligand excluded by PLIP EDO.43: 2 residues within 4Å: Chain F: Q.161, V.162 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain C: T.91, A.92, F.93, P.94 Chain F: K.117, A.118 Ligand excluded by PLIP EDO.45: 7 residues within 4Å: Chain F: G.19, M.20, L.21, A.68, G.71, D.72, V.78 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain F: A.163, N.164, M.167, C.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC 73102 at 2.00 A resolution. To be published

Release Date

2010-08-25

Peptides

creatinine amidohydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

creatinine amidohydrolase