SMTL ID : 4hgp.1

Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from Haemophilus influenzae in complex with transition state mimic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.14, D.16, D.107, D.111 Ligands: VN4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.14, A:D.16, A:D.107, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain B: D.14, D.16, D.107, D.111 Ligands: VN4.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.14, B:D.16, B:D.107, H2O.7, H2O.7 MG.7: 5 residues within 4Å: Chain C: D.14, D.16, D.107, D.111 Ligands: VN4.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.14, C:D.16, C:D.107, H2O.14, H2O.14 MG.10: 5 residues within 4Å: Chain D: D.14, D.16, D.107, D.111 Ligands: VN4.11 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.14, D:D.16, D:D.107, H2O.21, H2O.21

4 x VN4: oxido(dioxo)vanadium(Non-covalent)

VN4.2: 10 residues within 4Å: Chain A: D.14, V.15, D.16, S.58, G.59, K.84, D.107, V.110 Ligands: MG.1, KDO.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.15, A:D.16, A:G.59, A:K.84 Water bridges: A:S.58 VN4.5: 10 residues within 4Å: Chain B: D.14, V.15, D.16, S.58, G.59, K.84, D.107, V.110 Ligands: MG.4, KDO.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.15, B:D.16, B:G.59, B:K.84 Water bridges: B:S.58 VN4.8: 10 residues within 4Å: Chain C: D.14, V.15, D.16, S.58, G.59, K.84, D.107, V.110 Ligands: MG.7, KDO.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.15, C:D.16, C:G.59, C:K.84 Water bridges: C:S.58 VN4.11: 10 residues within 4Å: Chain D: D.14, V.15, D.16, S.58, G.59, K.84, D.107, V.110 Ligands: MG.10, KDO.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:V.15, D:D.16, D:G.59, D:K.84 Water bridges: D:S.58

4 x KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid(Non-covalent)

KDO.3: 14 residues within 4Å: Chain A: D.16, L.24, G.59, R.60, L.82 Chain D: V.38, G.41, L.42, K.45, R.68, L.72, M.178, G.179 Ligands: VN4.2 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:L.42, D:M.178, A:D.16, A:G.59, A:R.60 Salt bridges: D:R.68, A:R.60 KDO.6: 14 residues within 4Å: Chain B: D.16, L.24, G.59, R.60, L.82 Chain C: V.38, G.41, L.42, K.45, R.68, L.72, M.178, G.179 Ligands: VN4.5 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:D.16, B:G.59, B:R.60, C:L.42, C:M.178 Salt bridges: B:R.60, C:R.68 KDO.9: 14 residues within 4Å: Chain A: V.38, G.41, L.42, K.45, R.68, L.72, M.178, G.179 Chain C: D.16, L.24, G.59, R.60, L.82 Ligands: VN4.8 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:L.42, A:M.178, C:D.16, C:G.59, C:R.60 Salt bridges: A:R.68, C:R.60 KDO.12: 14 residues within 4Å: Chain B: V.38, G.41, L.42, K.45, R.68, L.72, M.178, G.179 Chain D: D.16, L.24, G.59, R.60, L.82 Ligands: VN4.11 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:L.42, B:M.178, D:D.16, D:G.59, D:R.60 Salt bridges: B:R.68, D:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daughtry, K.D. et al., Structural Basis for the Divergence of Substrate Specificity and Biological Function within HAD Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Biochemistry (2013)

Release Date

2013-08-21

Peptides

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC

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