SMTL ID : 3e81.2 (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 1.63 Å

Oligo State

homo-octamer

Ligands

8 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 MG.25: 4 residues within 4Å: Chain E: D.10, D.12, D.103 Ligands: VN4.30 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.24 MG.32: 4 residues within 4Å: Chain F: D.10, D.12, D.103 Ligands: VN4.36 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.10, F:D.12, F:D.103, H2O.29, H2O.29 MG.39: 4 residues within 4Å: Chain G: D.10, D.12, D.103 Ligands: VN4.43 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.10, G:D.12, G:D.103, H2O.32, H2O.32 MG.45: 5 residues within 4Å: Chain H: D.10, D.12, D.103, D.107 Ligands: VN4.48 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.10, H:D.12, H:D.103, H2O.37, H2O.37

12 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) PEG.26: 7 residues within 4Å: Chain E: R.62, A.65, E.66, V.70, D.71, Y.72, L.73 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.62, E:L.73, E:L.73 PEG.33: 2 residues within 4Å: Chain F: H.44, D.71 No protein-ligand interaction detected (PLIP) PEG.34: 6 residues within 4Å: Chain F: G.76, V.77, V.78, D.79, S.82, A.83 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.78, F:D.79, F:A.83 PEG.40: 3 residues within 4Å: Chain G: H.44, G.47, D.71 No protein-ligand interaction detected (PLIP) PEG.46: 6 residues within 4Å: Chain H: R.62, A.65, V.70, D.71, Y.72, L.73 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.62, H:L.73 PEG.47: 4 residues within 4Å: Chain H: F.74, A.83, E.86, L.87 No protein-ligand interaction detected (PLIP)

12 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 EDO.27: 4 residues within 4Å: Chain E: F.74, A.83, E.86, L.87 No protein-ligand interaction detected (PLIP) EDO.28: 3 residues within 4Å: Chain E: H.44, G.47, D.71 No protein-ligand interaction detected (PLIP) EDO.29: 1 residues within 4Å: Chain E: E.90 No protein-ligand interaction detected (PLIP) EDO.35: 1 residues within 4Å: Chain E: T.25 1 PLIP interactions: 1 interactions with chain E Water bridges: E:Q.24 EDO.41: 2 residues within 4Å: Chain G: R.62, E.66 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.62 EDO.42: 2 residues within 4Å: Chain E: F.41 Chain G: L.105 2 PLIP interactions: 2 interactions with chain G Water bridges: G:L.105, G:N.106

8 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 VN4.30: 9 residues within 4Å: Chain E: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: MG.25, SLB.31 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:I.11, E:D.12, E:D.12, E:D.12, E:G.55, E:K.80, E:N.106 Water bridges: E:T.54 VN4.36: 9 residues within 4Å: Chain F: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: MG.32, SLB.37 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:I.11, F:D.12, F:D.12, F:D.12, F:G.55, F:K.80, F:N.106 Water bridges: F:T.54 VN4.43: 9 residues within 4Å: Chain G: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: SLB.38, MG.39 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:I.11, G:D.12, G:D.12, G:T.54, G:G.55, G:K.80, G:N.106 VN4.48: 9 residues within 4Å: Chain H: D.10, I.11, D.12, T.54, G.55, K.80, N.106 Ligands: SLB.44, MG.45 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:I.11, H:D.12, H:D.12, H:T.54, H:G.55, H:K.80, H:N.106

8 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: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.68 Hydrogen bonds: B:S.37, B:S.37, B:K.67, B:K.67, A:D.12, A:E.56, A:E.56, A:E.56 Salt bridges: B:R.64, B:K.67 Water bridges: A:Y.22 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: 4 interactions with chain B, 8 interactions with chain D Hydrogen bonds: B:D.12, B:E.56, B:E.56, B:E.56, D:T.34, D:S.37, D:S.37, D:K.67 Hydrophobic interactions: D:L.68 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: 4 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:T.54, C:E.56, C:E.56, A:S.37, A:S.37, A:K.67 Water bridges: C:Y.22, A:L.68 Hydrophobic interactions: A:L.68 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: 7 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:L.68 Hydrogen bonds: C:T.34, C:S.37, C:S.37, C:K.67, D:T.54, D:G.55, D:E.56, D:E.56, D:E.56 Salt bridges: C:R.64, C:K.67 SLB.31: 11 residues within 4Å: Chain E: D.12, M.20, T.54, G.55, E.56 Chain F: T.34, S.37, R.64, K.67, L.68 Ligands: VN4.30 12 PLIP interactions: 5 interactions with chain E, 7 interactions with chain F Hydrogen bonds: E:D.12, E:E.56, E:E.56, E:E.56, F:S.37, F:S.37, F:K.67, F:K.67 Water bridges: E:Y.22 Hydrophobic interactions: F:L.68 Salt bridges: F:R.64, F:K.67 SLB.37: 11 residues within 4Å: Chain F: D.12, M.20, T.54, G.55, E.56 Chain H: T.34, S.37, R.64, K.67, L.68 Ligands: VN4.36 12 PLIP interactions: 8 interactions with chain H, 4 interactions with chain F Hydrophobic interactions: H:L.68 Hydrogen bonds: H:T.34, H:S.37, H:S.37, H:K.67, F:D.12, F:E.56, F:E.56, F:E.56 Water bridges: H:L.68 Salt bridges: H:R.64, H:K.67 SLB.38: 11 residues within 4Å: Chain E: T.34, S.37, R.64, K.67, L.68 Chain G: D.12, M.20, T.54, G.55, E.56 Ligands: VN4.43 11 PLIP interactions: 4 interactions with chain G, 7 interactions with chain E Hydrogen bonds: G:T.54, G:E.56, G:E.56, E:S.37, E:S.37, E:K.67 Water bridges: G:Y.22, E:L.68 Hydrophobic interactions: E:L.68 Salt bridges: E:R.64, E:K.67 SLB.44: 11 residues within 4Å: Chain G: T.34, S.37, R.64, K.67, L.68 Chain H: D.12, M.20, T.54, G.55, E.56 Ligands: VN4.48 12 PLIP interactions: 5 interactions with chain H, 7 interactions with chain G Hydrogen bonds: H:T.54, H:G.55, H:E.56, H:E.56, H:E.56, G:T.34, G:S.37, G:S.37, G:K.67 Hydrophobic interactions: G:L.68 Salt bridges: G:R.64, G: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: 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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