SMTL ID : 3h2z.1

The crystal structure of mannitol-1-phosphate dehydrogenase from Shigella flexneri

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 3 residues within 4Å: Chain A: G.9, N.10, I.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.10, A:I.11 Water bridges: A:G.9, A:G.12 ACT.2: 3 residues within 4Å: Chain A: F.265, D.266, K.269 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.266 Salt bridges: A:K.269 ACT.3: 4 residues within 4Å: Chain A: M.123, V.124, Q.129 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.124 Hydrogen bonds: A:V.124, A:Q.129 ACT.6: 2 residues within 4Å: Chain A: K.186, T.187 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.187 Salt bridges: A:K.186 ACT.15: 3 residues within 4Å: Chain B: G.9, N.10, I.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.10, B:I.11 Water bridges: B:G.9, B:G.12 ACT.16: 3 residues within 4Å: Chain B: F.265, D.266, K.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.266 Salt bridges: B:K.269 ACT.17: 4 residues within 4Å: Chain B: M.123, V.124, Q.129 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.124 Hydrogen bonds: B:V.124, B:Q.129 ACT.20: 2 residues within 4Å: Chain B: K.186, T.187 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.187 Salt bridges: B:K.186

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: E.93, N.136 Chain B: S.302, G.304, D.305 Ligands: ACT.17 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.302, B:S.302, B:G.304, B:D.305, A:N.136 GOL.18: 6 residues within 4Å: Chain A: S.302, G.304, D.305 Chain B: E.93, N.136 Ligands: ACT.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.302, A:S.302, A:G.304, B:N.136

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

NA.5: 1 residues within 4Å: Chain A: D.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.266 NA.7: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.369 NA.8: 1 residues within 4Å: Chain A: D.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.81 NA.9: 2 residues within 4Å: Chain A: K.18, R.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.18, A:R.159, A:R.159 Water bridges: A:D.22 NA.10: 3 residues within 4Å: Chain A: S.368, E.369, V.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.369, A:V.370 NA.19: 1 residues within 4Å: Chain B: D.266 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.266, B:D.266 NA.21: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.369 NA.22: 1 residues within 4Å: Chain B: D.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.81, B:D.81 NA.23: 2 residues within 4Å: Chain B: K.18, R.159 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.18, B:R.159, B:R.159 Water bridges: B:K.18 NA.24: 3 residues within 4Å: Chain B: S.368, E.369, V.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.369, B:V.370

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 5 residues within 4Å: Chain A: N.122, R.295, R.299, K.300, R.306 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.122, A:N.122 Water bridges: A:K.300, A:K.300, A:R.306 Salt bridges: A:R.299, A:K.300, A:R.306 PO4.12: 3 residues within 4Å: Chain A: R.245, K.249, Q.275 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.275, A:Q.275, A:Q.275 Salt bridges: A:R.245, A:K.249 PO4.13: 3 residues within 4Å: Chain A: T.202, D.203, N.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.201, A:T.202, A:D.203, A:N.204 PO4.14: 10 residues within 4Å: Chain A: F.6, G.7, A.30, D.31, V.32, S.68, V.87, V.91, R.94, I.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.7, A:V.32, A:S.68 Salt bridges: A:R.94 PO4.25: 5 residues within 4Å: Chain B: N.122, R.295, R.299, K.300, R.306 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.122, B:N.122 Water bridges: B:K.300, B:K.300, B:R.306 Salt bridges: B:R.299, B:K.300, B:R.306 PO4.26: 3 residues within 4Å: Chain B: R.245, K.249, Q.275 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.275, B:Q.275, B:Q.275 Salt bridges: B:R.245, B:K.249 PO4.27: 3 residues within 4Å: Chain B: T.202, D.203, N.204 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.201, B:T.202, B:T.202, B:D.203, B:N.204 PO4.28: 10 residues within 4Å: Chain B: F.6, G.7, A.30, D.31, V.32, S.68, V.87, V.91, R.94, I.95 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.7, B:V.32, B:S.68 Salt bridges: B:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., The crystal structure of mannitol-1-phosphate dehydrogenase from Shigella flexneri. To be Published

Release Date

2009-06-16

Peptides

Mannitol-1-phosphate 5-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Mannitol-1-phosphate 5-dehydrogenase