SMTL ID : 3tsc.1

Crystal structure of short chain dehydrogenase MAP_2410 from Mycobacterium paratuberculosis bound to NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: G.18, A.20, R.21, G.22, Q.23, D.42, I.43, L.47, Y.53, A.56, V.80, D.81, T.82, N.108, A.109, G.110, V.111, I.131, I.159, S.160, S.161, Y.174, K.178, P.204, G.205, P.206, V.207, T.209, P.210, M.211 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.204 Hydrogen bonds: A:R.21, A:Q.23, A:Q.23, A:I.43, A:D.81, A:T.82, A:N.108, A:G.110, A:K.178, A:V.207, A:V.207, A:T.209, A:T.209, A:M.211 Water bridges: A:G.24, A:A.56, A:A.56, A:N.108 Salt bridges: A:R.21 NAD.2: 31 residues within 4Å: Chain B: G.18, A.20, R.21, G.22, Q.23, D.42, I.43, L.47, Y.53, A.56, V.80, D.81, T.82, R.83, N.108, A.109, G.110, V.111, I.131, I.159, S.160, S.161, Y.174, K.178, P.204, G.205, P.206, V.207, T.209, P.210, M.211 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.204 Hydrogen bonds: B:R.21, B:Q.23, B:Q.23, B:I.43, B:D.81, B:D.81, B:T.82, B:N.108, B:G.110, B:Y.174, B:K.178, B:V.207, B:V.207, B:T.209, B:M.211 Water bridges: B:G.24, B:G.45, B:N.108 Salt bridges: B:R.21 NAD.3: 29 residues within 4Å: Chain C: G.18, A.20, R.21, G.22, Q.23, D.42, I.43, Y.53, A.56, V.80, D.81, T.82, N.108, A.109, G.110, V.111, I.131, I.159, S.160, S.161, Y.174, K.178, P.204, G.205, P.206, V.207, T.209, P.210, M.211 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.204 Hydrogen bonds: C:R.21, C:Q.23, C:Q.23, C:I.43, C:D.81, C:T.82, C:N.108, C:G.110, C:K.178, C:V.207, C:V.207, C:T.209, C:T.209, C:M.211 Water bridges: C:G.24, C:A.56, C:N.108 Salt bridges: C:R.21 NAD.6: 30 residues within 4Å: Chain D: G.18, R.21, G.22, Q.23, D.42, I.43, L.47, Y.53, A.56, V.80, D.81, T.82, R.83, N.108, A.109, G.110, V.111, I.131, I.159, S.160, S.161, Y.174, K.178, P.204, G.205, P.206, V.207, T.209, P.210, M.211 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.204 Hydrogen bonds: D:R.21, D:Q.23, D:Q.23, D:I.43, D:D.81, D:D.81, D:T.82, D:N.108, D:G.110, D:Y.174, D:K.178, D:V.207, D:V.207, D:T.209, D:M.211 Water bridges: D:G.24, D:A.56, D:N.108 Salt bridges: D:R.21

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 6 residues within 4Å: Chain C: Q.168, P.169, M.224, L.230, S.231, L.234 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.234 Hydrogen bonds: C:Q.168, C:S.231 MPD.5: 2 residues within 4Å: Chain C: D.86, R.87 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.86, C:R.87 Water bridges: C:R.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haft, D.H. et al., Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Sci Rep (2017)

Release Date

2011-10-05

Peptides

Putative oxidoreductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative oxidoreductase