SMTL ID : 4wec.2 (1 other biounit)

Crystal structure of a Short chain dehydrogenase from Mycobacterium smegmatis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Covalent)(Non-covalent)

NAD.1: 22 residues within 4Å: Chain A: G.37, A.39, S.40, G.41, I.42, D.61, I.62, V.81, D.82, V.83, N.109, A.110, G.111, T.161, A.162, S.163, Y.177, K.181, P.207, G.208, P.209, V.210 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.207, A:V.210 Hydrogen bonds: A:A.39, A:S.40, A:S.40, A:I.42, A:I.62, A:D.82, A:V.83, A:N.109, A:K.181, A:V.210, A:V.210 Water bridges: A:G.43, A:D.61, A:N.109, A:G.111, A:I.112 NAD.6: 22 residues within 4Å: Chain B: G.37, S.40, G.41, I.42, D.61, I.62, V.81, D.82, V.83, N.109, A.110, G.111, I.112, T.161, A.162, S.163, Y.177, K.181, P.207, G.208, P.209, V.210 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.207 Hydrogen bonds: B:S.40, B:S.40, B:S.40, B:S.40, B:I.42, B:I.62, B:D.82, B:D.82, B:V.83, B:N.109, B:Y.177, B:K.181, B:V.210, B:V.210 Water bridges: B:S.40, B:G.43, B:G.43, B:D.63, B:T.161 NAD.9: 23 residues within 4Å: Chain C: G.37, A.39, S.40, G.41, I.42, D.61, I.62, V.81, D.82, V.83, N.109, A.110, G.111, I.134, T.161, A.162, S.163, Y.177, K.181, P.207, G.208, P.209, V.210 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:P.207 Hydrogen bonds: C:A.39, C:S.40, C:S.40, C:I.42, C:I.62, C:D.82, C:D.82, C:V.83, C:N.109, C:Y.177, C:K.181, C:V.210, C:V.210 Water bridges: C:G.43, C:D.61, C:D.63, C:N.109, C:G.111, C:I.112, A:K.68, A:K.68 NAD.14: 23 residues within 4Å: Chain D: G.37, A.39, S.40, G.41, I.42, D.61, I.62, V.81, D.82, V.83, N.109, A.110, G.111, I.134, T.161, A.162, S.163, Y.177, K.181, P.207, G.208, P.209, V.210 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:P.207 Hydrogen bonds: D:S.40, D:S.40, D:S.40, D:S.40, D:I.42, D:I.62, D:D.82, D:V.83, D:N.109, D:K.181, D:V.210, D:V.210 Water bridges: D:G.43, D:D.61, D:N.109

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.232 Chain B: H.232 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.232, B:H.232, H2O.10, H2O.10, H2O.18, H2O.18 ZN.12: 2 residues within 4Å: Chain C: H.232 Chain D: H.232 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: D:H.232, C:H.232, H2O.28, H2O.29, H2O.38, H2O.38

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: S.113 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.113, A:S.113, H2O.5, H2O.9, H2O.13 MG.7: 1 residues within 4Å: Chain B: S.113 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.113, B:S.113 MG.10: 1 residues within 4Å: Chain C: S.113 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:S.113, C:S.113, H2O.26, H2O.28, H2O.32 MG.15: 1 residues within 4Å: Chain D: S.113 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.113, D:S.113, H2O.36, H2O.39, H2O.39

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

EDO.4: 6 residues within 4Å: Chain A: N.211, L.215, Q.216, F.219, R.237, F.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.215, A:F.238 Water bridges: A:G.236 EDO.5: 4 residues within 4Å: Chain A: S.262, T.263, F.264, L.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.262, A:L.265, A:L.265 EDO.8: 4 residues within 4Å: Chain B: N.211, Q.216, R.237, F.238 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.211, B:F.238 Water bridges: B:N.211, B:G.236 EDO.11: 5 residues within 4Å: Chain C: N.211, Q.216, F.219, R.237, F.238 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.211, C:L.215, C:F.238 EDO.13: 4 residues within 4Å: Chain C: S.262, T.263, F.264, L.265 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.262, C:L.265 Water bridges: C:T.263 EDO.16: 5 residues within 4Å: Chain D: N.211, Q.216, F.219, R.237, F.238 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal structure of a Short chain dehydrogenase from Mycobacterium smegmatis. to be published

Release Date

2014-10-08

Peptides

Short chain dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Short chain dehydrogenase

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