SMTL ID : 4hgo.1

2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron in complex with transition state mimic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.10, D.12, D.103 Ligands: VN4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.103, H2O.2, H2O.2 MG.4: 4 residues within 4Å: Chain B: D.10, D.12, D.103 Ligands: VN4.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.12, B:D.103, H2O.4, H2O.4 MG.6: 4 residues within 4Å: Chain C: D.10, D.12, D.103 Ligands: VN4.7 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:D.12, C:D.103, H2O.6, H2O.6 MG.8: 4 residues within 4Å: Chain D: D.10, D.12, D.103 Ligands: VN4.9 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:D.12, D:D.103, H2O.7, H2O.7

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

VN4.2: 9 residues within 4Å: Chain A: D.10, I.11, D.12, T.54, G.55, K.80, D.103 Ligands: MG.1, KDN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.11, A:D.12, A:D.12, A:T.54, A:G.55, A:K.80 VN4.5: 9 residues within 4Å: Chain B: D.10, I.11, D.12, T.54, G.55, K.80, D.103 Ligands: MG.4, KDN.10 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:I.11, B:D.12, B:T.54, B:G.55, B:K.80 Water bridges: D:T.34 VN4.7: 8 residues within 4Å: Chain C: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:I.11, C:D.12, C:D.12, C:D.12, C:G.55, C:K.80 Water bridges: C:T.54, C:N.106, C:N.106 VN4.9: 8 residues within 4Å: Chain D: D.10, I.11, D.12, T.54, G.55, K.80, D.103 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:I.11, D:D.12, D:D.12, D:G.55, D:K.80 Water bridges: D:T.54

2 x KDN: deamino-beta-neuraminic acid(Non-covalent)

KDN.3: 9 residues within 4Å: Chain A: D.12, M.20, E.56 Chain B: T.34, S.37, R.64, K.67, L.68 Ligands: VN4.2 14 PLIP interactions: 5 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:T.54, A:T.54, A:E.56, A:N.106, B:T.34, B:S.37, B:S.37, B:S.37, B:K.67, B:K.67 Water bridges: A:G.55 Hydrophobic interactions: B:L.68 Salt bridges: B:R.64, B:K.67 KDN.10: 10 residues within 4Å: Chain B: D.12, M.20, T.54, E.56 Chain D: T.34, S.37, R.64, K.67, L.68 Ligands: VN4.5 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: D:L.68 Hydrogen bonds: D:S.37, D:S.37, D:K.67, D:K.67, B:T.54, B:E.56, B:E.56 Salt bridges: D:R.64, D:K.67 Water bridges: B:Y.22, B:N.106

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

acylneuraminate cytidylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

acylneuraminate cytidylyltransferase

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