SMTL ID : 6ci9.4 (3 other biounits)

RMM microcompartment-associated aminopropanol dehydrogenase NADP + aminoacetone holo-structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 31 residues within 4Å: Chain A: G.16, S.18, K.19, G.20, I.21, G.40, R.41, N.42, A.65, D.66, V.67, N.93, A.94, G.95, I.96, F.97, V.116, T.143, S.144, S.145, Y.159, K.163, P.189, G.190, N.191, I.192, T.194, E.195, G.196, L.197 Ligands: F3V.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.21, A:P.189 Hydrogen bonds: A:S.18, A:S.18, A:K.19, A:K.19, A:I.21, A:R.41, A:R.41, A:N.42, A:D.66, A:V.67, A:N.93, A:N.93, A:G.95, A:Y.159, A:K.163, A:I.192, A:I.192, A:T.194, A:E.195, A:G.196 Water bridges: A:G.22, A:Q.166 Salt bridges: A:R.41 NAP.5: 31 residues within 4Å: Chain B: G.16, G.17, S.18, K.19, G.20, I.21, G.40, R.41, N.42, A.65, D.66, V.67, N.93, A.94, G.95, F.97, V.116, T.143, S.144, S.145, Y.159, K.163, P.189, G.190, N.191, I.192, T.194, E.195, G.196, L.197 Ligands: F3V.6 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:I.21, B:P.189 Hydrogen bonds: B:G.16, B:S.18, B:K.19, B:I.21, B:R.41, B:N.42, B:D.66, B:V.67, B:A.94, B:I.192, B:I.192, B:T.194, B:E.195, B:G.196 Water bridges: B:K.19, B:K.19, B:G.22, B:G.22, B:T.39, B:R.41, B:R.41, B:R.41, B:R.41, B:N.42, B:Q.166 Salt bridges: B:K.19, B:R.41 NAP.8: 31 residues within 4Å: Chain C: G.16, S.18, K.19, G.20, I.21, G.40, R.41, N.42, A.65, D.66, V.67, N.93, A.94, G.95, F.97, V.116, T.143, S.144, S.145, Y.159, K.163, P.189, G.190, N.191, I.192, T.194, E.195, G.196, L.197 Ligands: F3V.9, MG.11 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:I.21, C:P.189 Hydrogen bonds: C:G.16, C:S.18, C:K.19, C:I.21, C:R.41, C:N.42, C:D.66, C:V.67, C:N.93, C:N.93, C:I.192, C:I.192, C:T.194, C:E.195, C:E.195, C:G.196 Water bridges: C:S.18, C:S.18, C:G.22, C:R.41, C:R.41, C:D.45, C:Q.166 Salt bridges: C:R.41 NAP.12: 31 residues within 4Å: Chain D: G.16, S.18, K.19, G.20, I.21, G.40, R.41, N.42, A.65, D.66, V.67, N.93, A.94, G.95, I.96, F.97, V.116, T.143, S.144, S.145, Y.159, K.163, P.189, G.190, N.191, I.192, T.194, E.195, G.196, L.197 Ligands: F3V.13 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:I.21, D:P.189 Hydrogen bonds: D:G.16, D:S.18, D:K.19, D:I.21, D:R.41, D:N.42, D:D.66, D:V.67, D:N.93, D:Y.159, D:I.192, D:T.194, D:T.194, D:E.195, D:E.195, D:G.196 Water bridges: D:S.18, D:G.22, D:G.22, D:N.42, D:Q.166 Salt bridges: D:R.41

4 x F3V: 1-aminopropan-2-one(Non-covalent)

F3V.2: 11 residues within 4Å: Chain A: F.97, S.145, T.147, W.156, Y.159, G.190, N.191, L.197, Y.204 Chain C: E.253 Ligands: NAP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.97, A:W.156, A:Y.159, A:L.197 Hydrogen bonds: A:S.145, A:S.145, A:T.147, A:N.191, A:Y.204 F3V.6: 11 residues within 4Å: Chain B: F.97, S.145, T.147, W.156, Y.159, G.190, N.191, L.197, Y.204 Chain D: E.253 Ligands: NAP.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.97, B:W.156, B:Y.159, B:L.197 Hydrogen bonds: B:S.145, B:T.147, B:Y.159, B:N.191, D:E.253 F3V.9: 11 residues within 4Å: Chain A: E.253 Chain C: F.97, S.145, T.147, W.156, Y.159, G.190, N.191, L.197, Y.204 Ligands: NAP.8 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.97, C:W.156, C:Y.159, C:L.197 Hydrogen bonds: C:S.145, C:T.147, C:Y.159, C:N.191, A:E.253 F3V.13: 11 residues within 4Å: Chain B: E.253 Chain D: F.97, S.145, T.147, W.156, Y.159, G.190, N.191, L.197, Y.204 Ligands: NAP.12 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.97, D:W.156, D:L.197 Hydrogen bonds: D:S.145, D:T.147, B:E.253

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

CL.3: 4 residues within 4Å: Chain A: P.149, L.167, R.171 Ligands: CL.14 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: L.167, R.171 Ligands: CL.10 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: P.149, L.167, R.171 Ligands: CL.7 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain D: P.149, A.164, L.167, R.171 Ligands: CL.3 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 1 residues within 4Å: Chain A: E.8 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: NAP.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mallette, E. et al., Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis. Biochemistry (2018)

Release Date

2018-05-30

Peptides

3-oxoacyl-[acyl-carrier-protein] reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
O

D
P

3-oxoacyl-[acyl-carrier-protein] reductase

Related Entries With Identical Sequence