SMTL ID : 3e81.1 (1 other biounit)

Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 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: VN4.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.103, H2O.5, H2O.5 MG.8: 4 residues within 4Å: Chain B: D.10, D.12, D.103 Ligands: VN4.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.12, B:D.103, H2O.10, H2O.10 MG.15: 4 residues within 4Å: Chain C: D.10, D.12, D.103 Ligands: VN4.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.10, C:D.12, C:D.103, H2O.14, H2O.14 MG.21: 5 residues within 4Å: Chain D: D.10, D.12, D.103, D.107 Ligands: VN4.24 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:D.12, D:D.103, H2O.18, H2O.18

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 7 residues within 4Å: Chain A: R.62, A.65, E.66, V.70, D.71, Y.72, L.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.62, A:L.73, A:L.73 PEG.9: 2 residues within 4Å: Chain B: H.44, D.71 No protein-ligand interaction detected (PLIP) PEG.10: 6 residues within 4Å: Chain B: G.76, V.77, V.78, D.79, S.82, A.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.78, B:D.79, B:A.83 PEG.16: 3 residues within 4Å: Chain C: H.44, G.47, D.71 No protein-ligand interaction detected (PLIP) PEG.22: 6 residues within 4Å: Chain D: R.62, A.65, V.70, D.71, Y.72, L.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.62, D:L.73 PEG.23: 4 residues within 4Å: Chain D: F.74, A.83, E.86, L.87 No protein-ligand interaction detected (PLIP)

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

EDO.3: 4 residues within 4Å: Chain A: F.74, A.83, E.86, L.87 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: H.44, G.47, D.71 No protein-ligand interaction detected (PLIP) EDO.5: 1 residues within 4Å: Chain A: E.90 No protein-ligand interaction detected (PLIP) EDO.11: 1 residues within 4Å: Chain A: T.25 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.24 EDO.17: 2 residues within 4Å: Chain C: R.62, E.66 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.62 EDO.18: 2 residues within 4Å: Chain A: F.41 Chain C: L.105 2 PLIP interactions: 2 interactions with chain C Water bridges: C:L.105, C:N.106

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

VN4.6: 9 residues within 4Å: Chain A: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: MG.1, SLB.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.11, A:D.12, A:D.12, A:D.12, A:G.55, A:K.80, A:N.106 Water bridges: A:T.54 VN4.12: 9 residues within 4Å: Chain B: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: MG.8, SLB.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:I.11, B:D.12, B:D.12, B:D.12, B:G.55, B:K.80, B:N.106 Water bridges: B:T.54 VN4.19: 9 residues within 4Å: Chain C: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: SLB.14, MG.15 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:I.11, C:D.12, C:D.12, C:T.54, C:G.55, C:K.80, C:N.106 VN4.24: 9 residues within 4Å: Chain D: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: SLB.20, MG.21 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:I.11, D:D.12, D:D.12, D:T.54, D:G.55, D:K.80, D:N.106

4 x SLB: N-acetyl-beta-neuraminic acid(Non-covalent)

SLB.7: 11 residues within 4Å: Chain A: D.12, M.20, T.54, G.55, E.56 Chain B: T.34, S.37, R.64, K.67, L.68 Ligands: VN4.6 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:D.12, A:E.56, A:E.56, A:E.56, B:S.37, B:S.37, B:K.67, B:K.67 Water bridges: A:Y.22 Hydrophobic interactions: B:L.68 Salt bridges: B:R.64, B:K.67 SLB.13: 11 residues within 4Å: Chain B: D.12, M.20, T.54, G.55, E.56 Chain D: T.34, S.37, R.64, K.67, L.68 Ligands: VN4.12 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:L.68 Hydrogen bonds: D:T.34, D:S.37, D:S.37, D:K.67, B:D.12, B:E.56, B:E.56, B:E.56 Water bridges: D:L.68 Salt bridges: D:R.64, D:K.67 SLB.14: 11 residues within 4Å: Chain A: T.34, S.37, R.64, K.67, L.68 Chain C: D.12, M.20, T.54, G.55, E.56 Ligands: VN4.19 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.68 Hydrogen bonds: A:S.37, A:S.37, A:K.67, C:T.54, C:E.56, C:E.56 Water bridges: A:L.68, C:Y.22 Salt bridges: A:R.64, A:K.67 SLB.20: 11 residues within 4Å: Chain C: T.34, S.37, R.64, K.67, L.68 Chain D: D.12, M.20, T.54, G.55, E.56 Ligands: VN4.24 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:T.54, D:G.55, D:E.56, D:E.56, D:E.56, C:T.34, C:S.37, C:S.37, C:K.67 Hydrophobic interactions: C:L.68 Salt bridges: C:R.64, C:K.67

Links

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Citation

Lu, Z. et al., Structure-Function Analysis of 2-Keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate Phosphatase Defines Specificity Elements in Type C0 Haloalkanoate Dehalogenase Family Members. J.Biol.Chem. (2009)

Release Date

2008-11-04

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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