SMTL ID : 7ocq.1

NADH bound to the dehydrogenase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD from Acinetobacter baumannii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

1 x V8H: [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-4~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

V8H.1: 19 residues within 4Å: Chain A: G.251, F.252, G.253, A.254, I.255, T.280, R.281, C.335, L.336, P.337, E.344, I.372, L.373, N.374, V.414, R.416, M.417, V.418, K.420 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.255, A:V.414 Hydrogen bonds: A:F.252, A:A.254, A:I.255, A:T.280, A:R.281, A:E.344, A:N.374, A:V.418, A:V.418 Salt bridges: A:R.281

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.16, D.18, E.175, D.176 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:D.18, A:D.176 MG.14: 7 residues within 4Å: Chain B: D.16, D.18, E.25, G.54, E.175, D.176, S.177 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.16, B:D.18, B:D.176

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: D.16, S.119, K.151, E.175, S.177 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.119, A:S.177, A:S.177 Salt bridges: A:K.151 SO4.15: 6 residues within 4Å: Chain B: N.374, R.609, R.613, K.614, R.620 Ligands: NAI.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.374 Water bridges: B:N.532 Salt bridges: B:R.609, B:R.613, B:K.614, B:R.620 SO4.16: 5 residues within 4Å: Chain A: K.457 Chain B: R.281, N.282, K.420 Ligands: NAI.13 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.457, B:K.420 Hydrogen bonds: B:N.282, B:N.282

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

EDO.4: 4 residues within 4Å: Chain A: K.405, E.406, H.407, Y.408 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain A: K.8, N.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.169

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: R.90 Chain B: R.431 Ligands: CL.18 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.431, A:R.90, A:R.90 Water bridges: B:R.431 GOL.17: 5 residues within 4Å: Chain B: N.415, W.531, R.587, M.588, S.591 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.415, B:S.591, B:S.591

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

CL.7: 2 residues within 4Å: Chain A: R.613, R.620 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: L.373, N.374, V.413, V.414 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: G.99, Q.102, N.243, Q.244 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: D.610, P.611, L.612, L.653 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: R.428, R.431 Ligands: GOL.6 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: P.611, L.612 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: Y.547, E.548, S.549, V.552 Ligand excluded by PLIP

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 10 residues within 4Å: Chain A: I.130, N.133, Y.135 Chain B: R.298, L.421, N.425, Q.429, K.433, I.489, H.492 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.298, B:K.433 Hydrogen bonds: A:N.133, A:K.136 EPE.12: 11 residues within 4Å: Chain A: R.298, N.425, Q.429, I.489, H.492 Chain B: L.129, I.130, N.133, V.134, Y.135, K.136 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.133, B:Y.135, B:Y.135, B:Y.135, B:K.136, A:R.298 Salt bridges: A:R.298

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.13: 25 residues within 4Å: Chain B: G.251, F.252, G.253, A.254, I.255, S.279, T.280, R.281, C.335, L.336, P.337, A.340, E.344, I.372, L.373, N.374, V.414, R.416, M.417, V.418, K.420, R.606, R.609 Ligands: SO4.15, SO4.16 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.255, B:V.414 Hydrogen bonds: B:F.252, B:A.254, B:I.255, B:T.280, B:T.280, B:R.281, B:L.336, B:N.374, B:V.418, B:V.418, B:R.606, B:R.606 Salt bridges: B:K.420, B:R.609, B:R.609

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tam, H.K. et al., Unidirectional mannitol synthesis of Acinetobacter baumannii MtlD is facilitated by the helix-loop-helix-mediated dimer formation. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-04-20

Peptides

HAD hydrolase, family IA, variant 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HAD hydrolase, family IA, variant 3

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