SMTL ID : 7oct.1

NADPH bound to the dehydrogenase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD-N374A from Acinetobacter baumannii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.606, R.609, R.613, K.614, R.620 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.609, A:R.609, A:R.613, A:R.613, A:K.614, A:R.620 EDO.3: 4 residues within 4Å: Chain A: K.405, E.406, H.407, Y.408 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: S.422, N.423 Chain B: K.457 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.423

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.16, D.18, E.175, D.176 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.18, A:D.176, H2O.1 MG.11: 8 residues within 4Å: Chain B: D.16, D.18, E.25, G.54, E.175, D.176, S.177 Ligands: SO4.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.16, B:D.18, B:E.175, B:D.176

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.5: 23 residues within 4Å: Chain A: G.251, F.252, G.253, A.254, I.255, S.279, T.280, R.281, N.282, C.335, L.336, P.337, A.340, E.344, I.372, L.373, A.374, V.414, R.416, M.417, V.418, K.420 Ligands: SO4.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.255, A:V.414 Hydrogen bonds: A:G.251, A:A.254, A:I.255, A:T.280, A:R.281, A:R.281, A:R.281, A:N.282, A:L.336, A:A.374, A:V.418, A:V.418 Salt bridges: A:R.281, A:K.420 pi-Cation interactions: A:R.281 NDP.15: 26 residues within 4Å: Chain B: G.251, F.252, G.253, A.254, I.255, T.280, R.281, N.282, C.335, L.336, P.337, A.340, S.343, E.344, I.372, L.373, A.374, V.414, R.416, M.417, V.418, K.420, R.606, R.609 Ligands: SO4.16, SO4.17 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.255, B:I.255, B:V.414 Hydrogen bonds: B:G.251, B:A.254, B:I.255, B:T.280, B:R.281, B:R.281, B:N.282, B:L.336, B:S.343, B:E.344, B:A.374, B:V.418, B:V.418, B:R.606 Salt bridges: B:K.420, B:K.420, B:R.609, B:R.609

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

SO4.6: 7 residues within 4Å: Chain A: L.373, A.374, T.412, V.413, V.414, K.527 Ligands: NDP.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.414 Water bridges: A:A.374, A:Q.524, A:Q.524 Salt bridges: A:K.527 SO4.7: 5 residues within 4Å: Chain A: D.610, P.611, L.612, L.653, I.655 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.612 SO4.12: 10 residues within 4Å: Chain B: D.16, M.17, D.18, E.25, G.54, T.118, S.119, K.151, E.175 Ligands: MG.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:M.17, B:D.18, B:E.25, B:R.28, B:G.54, B:T.118, B:T.118, B:S.119 Salt bridges: B:K.151 SO4.16: 7 residues within 4Å: Chain B: P.337, R.609, D.610, R.613, K.614, R.620 Ligands: NDP.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.610, B:R.620, B:R.620 Salt bridges: B:R.609, B:R.613, B:K.614 SO4.17: 8 residues within 4Å: Chain B: L.373, A.374, T.412, V.413, V.414, K.527, N.532 Ligands: NDP.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.414, B:N.532 Salt bridges: B:K.527 SO4.19: 7 residues within 4Å: Chain B: D.610, P.611, L.612, R.613, A.649, L.653, I.655 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.612, B:R.613

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

CL.8: 4 residues within 4Å: Chain A: G.99, Q.102, N.243, Q.244 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: R.428, R.431 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.9: 1 residues within 4Å: Chain A: D.223 No protein-ligand interaction detected (PLIP)

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

EPE.10: 11 residues within 4Å: Chain A: I.130, N.133, Y.135, K.136 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.18: 12 residues within 4Å: Chain A: R.298, L.421, N.425, Q.429, K.433, I.489, H.492 Chain B: L.129, I.130, N.133, V.134, Y.135 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.425, B:V.134, B:Y.135 Salt bridges: A:R.298, A:K.433

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 5 residues within 4Å: Chain A: Q.163 Chain B: Y.547, E.548, S.549, V.552 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.163, B:E.548, B:S.549 ACT.14: 7 residues within 4Å: Chain B: L.352, R.355, F.356, H.402, I.403, E.406, H.407 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.356 Salt bridges: B:H.402, B:H.407

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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