SMTL ID : 7ocr.1

NADPH and fructose-6-phosphate 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 2.60 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: D.16, S.119, K.151, S.177, G.180 Ligands: MG.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.119, A:S.119, A:S.177, A:G.180 Salt bridges: A:K.151 SO4.2: 5 residues within 4Å: Chain A: N.374, K.375, R.613, K.614, R.620 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.375, A:R.613, A:K.614, A:R.620

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

NDP.3: 19 residues within 4Å: Chain A: G.251, F.252, G.253, A.254, I.255, T.280, R.281, N.282, C.335, L.336, P.337, A.340, E.344, L.373, N.374, V.414, R.416, V.418, K.420 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.255 Hydrogen bonds: A:G.251, A:A.254, A:I.255, A:T.280, A:R.281, A:R.281, A:N.282, A:L.336, A:S.343, A:E.344, A:N.374, A:V.418, A:V.418 Salt bridges: A:R.281, A:K.420, A:K.420 pi-Cation interactions: A:R.281 NDP.21: 25 residues within 4Å: Chain B: 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, N.374, V.414, R.416, M.417, V.418, K.420, R.606, R.609 Ligands: F6R.22 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.255 Hydrogen bonds: B:A.254, B:I.255, B:S.279, B:T.280, B:T.280, B:R.281, B:R.281, B:N.282, B:L.336, B:N.374, B:V.418, B:V.418, B:R.606 Water bridges: B:K.420 Salt bridges: B:K.420, B:R.609, B:R.609

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

EPE.4: 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: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.425, A:K.136 Salt bridges: B:R.298, B:K.433 EPE.13: 11 residues within 4Å: Chain A: R.298, L.421, N.425, Q.429, K.433, I.489, H.492 Chain B: I.130, N.133, Y.135, K.136 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.425, B:K.136 Salt bridges: A:R.298

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

EDO.5: 5 residues within 4Å: Chain A: M.50, K.195, I.197, K.198, E.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.195, A:E.199 EDO.6: 4 residues within 4Å: Chain A: K.405, E.406, H.407, Y.408 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: M.231, P.498, V.515, R.587 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: L.27, Q.30, T.31, Q.34, H.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.30, A:Q.34, A:M.84 EDO.19: 6 residues within 4Å: Chain B: S.56, A.57, S.119, R.121, G.144, D.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.119, B:D.145 EDO.20: 4 residues within 4Å: Chain B: P.634, Y.635, K.636, E.684 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.635, B:E.684

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

CL.9: 5 residues within 4Å: Chain A: L.373, N.374, V.413, V.414 Ligands: CL.11 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: S.119, G.150, K.151, I.156 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: N.374, K.375, Q.524 Ligands: CL.9 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: G.99, Q.102, N.243, Q.244 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: Y.547, E.548, S.549, V.552 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: P.611, L.612 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: G.99, Q.102, N.243, Q.244 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 5 residues within 4Å: Chain A: D.16, D.18, E.175, D.176 Ligands: SO4.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:D.18, A:D.176 MG.23: 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

1 x K: POTASSIUM ION(Non-covalent)

K.15: 1 residues within 4Å: Chain A: D.223 No protein-ligand interaction detected (PLIP)

1 x F6R: FRUCTOSE -6-PHOSPHATE(Non-covalent)

F6R.22: 15 residues within 4Å: Chain B: N.374, N.415, R.416, M.417, K.527, W.531, N.532, H.535, R.606, V.607, R.609, R.613, K.614, R.620 Ligands: NDP.21 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.374, B:N.415, B:K.527, B:N.532, B:H.535, B:R.606, B:R.606 Salt bridges: B:R.609, B:R.613, B:K.614, B:R.620

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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