SMTL ID : 7ocs.2 (1 other biounit)

Mannitol-1-phosphate bound to the phosphatase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD-D16A from Acinetobacter baumannii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: K.379, Y.380, M.383 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.380 EDO.2: 3 residues within 4Å: Chain A: H.153, E.155, L.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.155 EDO.3: 3 residues within 4Å: Chain A: K.8, H.209, F.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.209 EDO.4: 9 residues within 4Å: Chain A: K.379, H.407, Y.408, F.409, C.410, E.502, K.503, G.504, S.505 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.409, A:F.409, A:E.502 Water bridges: A:E.502, A:K.503

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

EPE.5: 13 residues within 4Å: Chain A: L.129, I.130, N.133, Y.135, K.136 Chain B: R.298, L.421, N.425, Q.429, K.433, I.489, H.492 Ligands: CL.21 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:N.425, B:R.428 Salt bridges: B:R.298 Hydrogen bonds: A:N.133, A:Y.135, A:K.136

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

SO4.6: 6 residues within 4Å: Chain A: N.374, K.375, V.376, T.412, Q.524, K.527 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.375, A:Q.524 Salt bridges: A:K.527 SO4.7: 3 residues within 4Å: Chain A: R.609, K.614, R.620 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.609, A:R.620 Salt bridges: A:R.609, A:R.620 SO4.8: 3 residues within 4Å: Chain A: G.253, A.254, K.420 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.254 Water bridges: A:I.255 SO4.18: 7 residues within 4Å: Chain B: S.56, A.57, T.58, S.119, R.121, G.144, D.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.57, B:T.58, B:S.119 Water bridges: B:R.121

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

CL.9: 4 residues within 4Å: Chain A: G.99, Q.102, N.243, Q.244 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: Y.48, Q.51 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: F.356 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: T.58, G.144, D.145 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: G.99, Q.102, N.243, Q.244 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: N.374, Q.524, K.527 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain A: Y.135 Chain B: R.298, H.492 Ligands: EPE.5 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.13: 2 residues within 4Å: Chain A: R.106, D.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.223 Water bridges: A:R.106 NA.22: 3 residues within 4Å: Chain B: R.106, D.268, K.510 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.106, B:D.268, B:D.268 Water bridges: B:D.223

2 x 44H: D-Mannitol-1-phosphate(Non-covalent)

44H.14: 16 residues within 4Å: Chain A: A.16, M.17, D.18, E.25, R.28, L.32, C.52, L.53, G.54, L.55, R.78, T.118, S.119, S.120, K.151, D.176 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:M.17, A:D.18, A:D.18, A:R.28, A:R.28, A:G.54, A:L.55, A:T.118, A:S.119, A:S.120 Water bridges: A:D.18, A:E.25, A:E.25, A:R.78, A:K.151, A:K.151 Salt bridges: A:K.151 44H.23: 16 residues within 4Å: Chain B: A.16, M.17, D.18, E.25, R.28, L.32, C.52, L.53, G.54, L.55, R.78, T.118, S.119, S.120, K.151, D.176 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:M.17, B:D.18, B:R.28, B:R.28, B:G.54, B:L.55, B:Y.74, B:R.78, B:T.118, B:S.119, B:S.120, B:D.176 Water bridges: B:E.25, B:S.177 Salt bridges: B:K.151

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.15: 14 residues within 4Å: Chain A: R.298, L.421, N.425, R.428, Q.429, K.433, I.489, H.492 Chain B: L.129, I.130, N.133, V.134, Y.135, K.136 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:Y.135, B:K.136, A:R.298, A:R.298, A:H.492 Water bridges: A:N.425, A:R.428, A:Q.429

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 4 residues within 4Å: Chain B: K.405, E.406, H.407, Y.408 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.405, B:K.405

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

ACT.17: 7 residues within 4Å: Chain B: H.250, G.251, S.279, R.281, S.316, L.336, E.344 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.336, B:E.344 Hydrogen bonds: B:S.316 Water bridges: B:F.252, B:T.280 Salt bridges: B:R.281

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

2022-04-27

Peptides

HAD hydrolase, family IA, variant 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

HAD hydrolase, family IA, variant 3

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