SMTL ID : 3e84.2 (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 1.85 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.10, D.12, D.103, D.107 Ligands: WO4.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.103, H2O.4, H2O.8 MG.6: 5 residues within 4Å: Chain B: D.10, D.12, D.103, D.107 Ligands: WO4.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.10, B:D.12, B:D.103, H2O.2, H2O.14 MG.9: 5 residues within 4Å: Chain C: D.10, D.12, D.103, D.107 Ligands: WO4.10 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.12: 4 residues within 4Å: Chain D: D.10, D.12, D.103 Ligands: WO4.13 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.10, D:D.12, D:D.103, H2O.11, H2O.12 MG.14: 5 residues within 4Å: Chain E: D.10, D.12, D.103, D.107 Ligands: WO4.15 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.10, E:D.12, E:D.103, H2O.23, H2O.28 MG.19: 5 residues within 4Å: Chain F: D.10, D.12, D.103, D.107 Ligands: WO4.20 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.10, F:D.12, F:D.103, H2O.21, H2O.33 MG.22: 5 residues within 4Å: Chain G: D.10, D.12, D.103, D.107 Ligands: WO4.23 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.10, G:D.12, G:D.103, H2O.25, H2O.25 MG.25: 4 residues within 4Å: Chain H: D.10, D.12, D.103 Ligands: WO4.26 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.10, H:D.12, H:D.103, H2O.31, H2O.31

8 x WO4: TUNGSTATE(VI)ION(Non-covalent)

WO4.2: 9 residues within 4Å: Chain A: D.10, I.11, D.12, T.54, G.55, E.56, K.80, N.106 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:I.11, A:D.12, A:D.12, A:T.54, A:G.55, A:E.56, A:E.56, A:K.80, A:N.106 Water bridges: A:T.54 Metal complexes: A:D.10 WO4.7: 9 residues within 4Å: Chain B: D.10, I.11, D.12, T.54, G.55, E.56, K.80, N.106 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:I.11, B:D.12, B:D.12, B:T.54, B:G.55, B:E.56, B:K.80, B:N.106 Water bridges: B:T.54, B:E.56 Metal complexes: B:D.10 WO4.10: 10 residues within 4Å: Chain C: D.10, I.11, D.12, T.54, G.55, E.56, K.80, D.103, N.106 Ligands: MG.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:I.11, C:D.12, C:T.54, C:T.54, C:G.55, C:E.56, C:K.80, C:N.106 Metal complexes: C:D.10 WO4.13: 10 residues within 4Å: Chain D: D.10, I.11, D.12, T.54, G.55, E.56, K.80, D.103, N.106 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:I.11, D:D.12, D:T.54, D:T.54, D:G.55, D:E.56, D:K.80, D:N.106 Metal complexes: D:D.10 WO4.15: 9 residues within 4Å: Chain E: D.10, I.11, D.12, T.54, G.55, E.56, K.80, N.106 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:I.11, E:D.12, E:D.12, E:T.54, E:G.55, E:E.56, E:E.56, E:K.80, E:N.106 Water bridges: E:T.54 Metal complexes: E:D.10 WO4.20: 9 residues within 4Å: Chain F: D.10, I.11, D.12, T.54, G.55, E.56, K.80, N.106 Ligands: MG.19 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:I.11, F:D.12, F:D.12, F:T.54, F:G.55, F:E.56, F:K.80, F:N.106 Water bridges: F:T.54, F:E.56 Metal complexes: F:D.10 WO4.23: 10 residues within 4Å: Chain G: D.10, I.11, D.12, T.54, G.55, E.56, K.80, D.103, N.106 Ligands: MG.22 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:I.11, G:D.12, G:T.54, G:T.54, G:G.55, G:E.56, G:K.80, G:N.106 Metal complexes: G:D.10 WO4.26: 10 residues within 4Å: Chain H: D.10, I.11, D.12, T.54, G.55, E.56, K.80, D.103, N.106 Ligands: MG.25 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:I.11, H:D.12, H:T.54, H:T.54, H:G.55, H:E.56, H:K.80, H:N.106 Metal complexes: H:D.10

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

PEG.3: 3 residues within 4Å: Chain A: H.44, G.47, D.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.47 PEG.4: 5 residues within 4Å: Chain A: F.74, S.82, A.83, E.86, L.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.82 PEG.8: 3 residues within 4Å: Chain B: H.44, G.47, D.71 No protein-ligand interaction detected (PLIP) PEG.11: 4 residues within 4Å: Chain C: H.44, G.47, P.49, D.71 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.47 PEG.16: 3 residues within 4Å: Chain E: H.44, G.47, D.71 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.47 PEG.17: 5 residues within 4Å: Chain E: F.74, S.82, A.83, E.86, L.87 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.82 PEG.21: 3 residues within 4Å: Chain F: H.44, G.47, D.71 No protein-ligand interaction detected (PLIP) PEG.24: 4 residues within 4Å: Chain G: H.44, G.47, P.49, D.71 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.47

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

EDO.5: 4 residues within 4Å: Chain A: A.123, P.124, F.125 Chain F: F.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.125 EDO.18: 4 residues within 4Å: Chain B: F.134 Chain E: A.123, P.124, F.125 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:F.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Acylneuraminate cytidylyltransferase

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