SMTL ID : 7ocs.1 (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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Q.102, R.106, Y.216, L.219, T.220, D.223, P.506, L.507 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.106, A:D.223 Water bridges: A:Q.102, A:Q.102

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

EDO.2: 2 residues within 4Å: Chain A: Q.65, V.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.65 EDO.3: 6 residues within 4Å: Chain A: R.355, F.356, S.358, C.363, I.364 Ligands: CL.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.363 EDO.4: 5 residues within 4Å: Chain A: P.366, K.405, E.406, H.407, Y.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.406 EDO.5: 4 residues within 4Å: Chain A: K.571, Q.572, A.575, I.576 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.572 EDO.6: 7 residues within 4Å: Chain A: M.417, V.418, S.419, H.492, S.493, E.494, K.601 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.419, A:E.494, A:K.601 EDO.20: 3 residues within 4Å: Chain B: H.6, G.7, F.225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.6 EDO.21: 4 residues within 4Å: Chain B: L.205, E.206, A.208, H.209 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.206, B:A.208 EDO.22: 7 residues within 4Å: Chain B: M.417, V.418, S.419, H.492, S.493, E.494, K.601 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.494, B:K.601, B:K.601 Water bridges: B:S.493 EDO.23: 5 residues within 4Å: Chain A: R.431 Chain B: L.86, E.87, R.90, E.127 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.431, B:E.127

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 8 residues within 4Å: Chain A: V.2, L.3, V.10, H.11, K.109, S.110, G.111, L.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.3, A:S.110 PGE.8: 13 residues within 4Å: Chain A: R.298, K.420, L.421, S.422, N.425, R.428, Q.429, K.433, I.489, H.492, K.601 Chain B: I.130, Y.135 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.422, A:N.425, A:K.433 Water bridges: A:R.298, A:R.428

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

PG4.9: 14 residues within 4Å: Chain A: L.129, I.130, N.133, V.134, Y.135, K.136 Chain B: R.298, L.421, N.425, R.428, Q.429, K.433, I.489, H.492 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.298, B:R.298, B:N.425, B:R.428, A:N.133, A:Y.135, A:K.136 Water bridges: B:Q.429

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.10: 9 residues within 4Å: Chain A: H.250, G.251, S.279, T.280, R.281, S.316, L.336, P.337, E.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.251, A:S.316 BME.24: 4 residues within 4Å: Chain B: R.80, E.83, M.84, E.87 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.80

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

SO4.11: 6 residues within 4Å: Chain A: D.610, P.611, L.612, R.613, L.653, I.655 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.610, A:L.612, A:R.613 SO4.12: 9 residues within 4Å: Chain A: L.373, N.374, K.375, V.376, T.412, V.413, Q.524, K.527 Ligands: MG.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.375, A:K.375, A:Q.524 Water bridges: A:N.532 SO4.13: 6 residues within 4Å: Chain A: N.374, K.375, R.609, R.613, K.614, R.620 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.374, A:R.609 Water bridges: A:K.614 Salt bridges: A:K.375, A:R.613, A:K.614, A:R.620 SO4.14: 7 residues within 4Å: Chain A: S.56, A.57, T.58, S.119, R.121, G.144, D.145 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.57, A:T.58, A:T.58, A:S.119 Water bridges: A:R.121, A:R.121 SO4.25: 5 residues within 4Å: Chain B: K.375, V.376, V.413, Q.524, K.527 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.375, B:Q.524 Water bridges: B:K.375, B:V.414 SO4.26: 6 residues within 4Å: Chain B: S.56, A.57, T.58, S.119, G.144, D.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.56, B:S.56, B:A.57, B:T.58

1 x MG: MAGNESIUM ION(Non-covalent)

MG.15: 6 residues within 4Å: Chain A: I.371, L.373, A.378, D.411, T.412 Ligands: SO4.12 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.373, A:T.412, H2O.4

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

CL.16: 4 residues within 4Å: Chain A: G.99, Q.102, N.243, Q.244 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: F.356, E.406 Ligands: EDO.3 Ligand excluded by PLIP CL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

44H.19: 15 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, T.118, S.119, S.120, K.151, D.176 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:M.17, A:D.18, A:R.28, A:R.28, A:G.54, A:L.55, A:S.119, A:S.120, A:D.176 Water bridges: A:D.18, A:E.25, A:R.78, A:R.78, A:K.151, A:K.151 Salt bridges: A:K.151 44H.27: 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 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:M.17, B:D.18, B:D.18, B:E.25, B:R.28, B:R.28, B:G.54, B:L.55, B:L.55, B:R.78, B:A.117, B:S.119, B:S.120, B:D.176 Water bridges: B:R.78, B:R.78 Salt bridges: B:K.151

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
A

B
D

HAD hydrolase, family IA, variant 3

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