SMTL ID : 3pk0.2 (1 other biounit)

Crystal structure of Short-chain dehydrogenase/reductase SDR from Mycobacterium smegmatis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: F.99, Y.155, W.158, Y.161 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.255 Water bridges: A:S.147, A:N.193 GOL.5: 7 residues within 4Å: Chain A: I.22, N.95, A.96, G.97, T.145, Y.161, K.165 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.95, A:N.95, A:Y.161, A:Y.161 Water bridges: A:I.22, A:G.23, A:K.165 GOL.6: 4 residues within 4Å: Chain B: F.99, Y.155, W.158, Y.161 3 PLIP interactions: 3 interactions with chain D Water bridges: D:E.255, D:E.255, D:E.255 GOL.9: 7 residues within 4Å: Chain B: I.22, N.95, A.96, G.97, T.145, Y.161, K.165 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.95, B:Y.161 Water bridges: B:I.22, B:G.23, B:Y.161, B:K.165 GOL.10: 4 residues within 4Å: Chain C: F.99, Y.155, W.158, Y.161 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:E.255 Water bridges: A:E.255, A:E.255, C:T.149, C:T.149, C:N.193 GOL.14: 7 residues within 4Å: Chain C: I.22, N.95, A.96, G.97, T.145, Y.161, K.165 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.95, C:N.95, C:Y.161 Water bridges: C:I.22, C:G.23, C:Y.161, C:K.165 GOL.15: 4 residues within 4Å: Chain D: F.99, Y.155, W.158, Y.161 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:N.193, B:E.255 GOL.18: 7 residues within 4Å: Chain D: I.22, N.95, A.96, G.97, T.145, Y.161, K.165 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.95, D:Y.161, D:Y.161 Water bridges: D:I.22, D:G.23, D:K.165

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 1 residues within 4Å: Chain A: D.101 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.101, H2O.3, H2O.8 CA.4: 3 residues within 4Å: Chain A: D.55, G.58, G.60 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.55, A:D.55, A:G.58, A:G.60, H2O.3, H2O.5 CA.8: 3 residues within 4Å: Chain B: D.55, G.58, G.60 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.55, B:D.55, B:G.58, B:G.60, H2O.11 CA.11: 1 residues within 4Å: Chain C: D.101 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.101, H2O.20, H2O.25 CA.13: 3 residues within 4Å: Chain C: D.55, G.58, G.60 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.55, C:D.55, C:G.58, C:G.60, H2O.20, H2O.22 CA.17: 3 residues within 4Å: Chain D: D.55, G.58, G.60 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.55, D:D.55, D:G.58, D:G.60, H2O.28

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

CL.3: 3 residues within 4Å: Chain A: L.169, R.173 Ligands: CL.7 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: A.166, L.169, R.173 Ligands: CL.3 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: L.169, R.173 Ligands: CL.16 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: A.166, L.169, R.173 Ligands: CL.12 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2015)

Release Date

2010-11-24

Peptides

Short-chain dehydrogenase/reductase SDR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
B

D
D

Short-chain dehydrogenase/reductase SDR

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