SMTL ID : 3e8m.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 1.10 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, G.13, D.103, D.104 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.103, H2O.1, H2O.1, H2O.1 MG.12: 5 residues within 4Å: Chain B: D.10, D.12, G.13, D.103, D.104 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.10, B:D.12, B:D.103, H2O.12, H2O.12, H2O.12 MG.19: 5 residues within 4Å: Chain C: D.10, D.12, G.13, D.103, D.104 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.10, C:D.12, C:D.103, H2O.22, H2O.22, H2O.22 MG.25: 5 residues within 4Å: Chain D: D.10, D.12, G.13, D.103, D.104 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.10, D:D.12, D:D.103, H2O.33, H2O.33, H2O.33 MG.33: 5 residues within 4Å: Chain E: D.10, D.12, G.13, D.103, D.104 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.10, E:D.12, E:D.103, H2O.43, H2O.43, H2O.43 MG.44: 5 residues within 4Å: Chain F: D.10, D.12, G.13, D.103, D.104 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.10, F:D.12, F:D.103, H2O.54, H2O.54, H2O.54 MG.51: 5 residues within 4Å: Chain G: D.10, D.12, G.13, D.103, D.104 6 PLIP interactions: 3 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.10, G:D.12, G:D.103, H2O.64, H2O.64, H2O.64 MG.57: 5 residues within 4Å: Chain H: D.10, D.12, G.13, D.103, D.104 6 PLIP interactions: 3 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.10, H:D.12, H:D.103, H2O.75, H2O.75, H2O.75

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: D.10, T.54, G.55, E.56, K.80, N.106 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: F.21 Chain B: F.21 Chain C: F.21 Chain D: F.21 Ligands: PG4.8 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: D.10, T.54, G.55, E.56, K.80, N.106 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain C: D.10, T.54, G.55, E.56, K.80, N.106 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain D: D.10, T.54, G.55, E.56, K.80, N.106 Ligand excluded by PLIP CL.34: 6 residues within 4Å: Chain E: D.10, T.54, G.55, E.56, K.80, N.106 Ligand excluded by PLIP CL.35: 5 residues within 4Å: Chain E: F.21 Chain F: F.21 Chain G: F.21 Chain H: F.21 Ligands: PG4.40 Ligand excluded by PLIP CL.45: 6 residues within 4Å: Chain F: D.10, T.54, G.55, E.56, K.80, N.106 Ligand excluded by PLIP CL.52: 6 residues within 4Å: Chain G: D.10, T.54, G.55, E.56, K.80, N.106 Ligand excluded by PLIP CL.58: 6 residues within 4Å: Chain H: D.10, T.54, G.55, E.56, K.80, N.106 Ligand excluded by PLIP

12 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 8 residues within 4Å: Chain A: T.34, S.37, R.64, K.67, L.68 Chain C: M.20, Y.22, E.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.34 Water bridges: A:K.67 Salt bridges: A:R.64, A:K.67 ACY.5: 7 residues within 4Å: Chain A: F.125, R.128, R.129 Chain F: F.125, R.128, R.129, F.134 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:R.129 Water bridges: A:R.128, A:R.128, A:R.128, F:R.128 Salt bridges: A:R.128, F:R.128 ACY.14: 8 residues within 4Å: Chain A: M.20, Y.22, E.56 Chain B: T.34, S.37, R.64, K.67, L.68 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.34, B:T.34 Water bridges: B:K.67 Salt bridges: B:R.64, B:K.67 ACY.21: 8 residues within 4Å: Chain C: T.34, S.37, R.64, K.67, L.68 Chain D: M.20, Y.22, E.56 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.34, C:T.34 Water bridges: C:K.67 Salt bridges: C:R.64, C:K.67 ACY.27: 7 residues within 4Å: Chain B: M.20, E.56 Chain D: T.34, S.37, R.64, K.67, L.68 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.34, D:S.37 Water bridges: D:K.67 Salt bridges: D:R.64, D:K.67 ACY.28: 7 residues within 4Å: Chain D: F.125, R.128, R.129 Chain G: F.125, R.128, R.129, F.134 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain G Hydrophobic interactions: D:R.129 Water bridges: D:R.128, G:R.128, G:R.128, G:R.128 Salt bridges: D:R.128, G:R.128 ACY.36: 8 residues within 4Å: Chain E: T.34, S.37, R.64, K.67, L.68 Chain G: M.20, Y.22, E.56 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.34 Water bridges: E:K.67 Salt bridges: E:R.64, E:K.67 ACY.37: 7 residues within 4Å: Chain B: F.125, R.128, R.129, F.134 Chain E: F.125, R.128, R.129 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:R.129 Water bridges: E:R.128, E:R.128, E:R.128, B:R.128 Salt bridges: E:R.128, B:R.128 ACY.46: 8 residues within 4Å: Chain E: M.20, Y.22, E.56 Chain F: T.34, S.37, R.64, K.67, L.68 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:T.34, F:T.34 Water bridges: F:K.67 Salt bridges: F:R.64, F:K.67 ACY.53: 8 residues within 4Å: Chain G: T.34, S.37, R.64, K.67, L.68 Chain H: M.20, Y.22, E.56 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:T.34, G:T.34 Water bridges: G:K.67 Salt bridges: G:R.64, G:K.67 ACY.59: 7 residues within 4Å: Chain F: M.20, E.56 Chain H: T.34, S.37, R.64, K.67, L.68 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:T.34, H:S.37 Water bridges: H:K.67 Salt bridges: H:R.64, H:K.67 ACY.60: 7 residues within 4Å: Chain C: F.125, R.128, R.129, F.134 Chain H: F.125, R.128, R.129 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain C Hydrophobic interactions: H:R.129 Water bridges: H:R.128, C:R.128, C:R.128, C:R.128 Salt bridges: H:R.128, C:R.128

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

PEG.6: 5 residues within 4Å: Chain A: H.44, G.47, I.48, P.49, D.71 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.47, A:D.71 PEG.7: 6 residues within 4Å: Chain A: Y.72, F.74, A.83, E.86, L.87, E.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.87 PEG.15: 5 residues within 4Å: Chain B: H.44, G.47, I.48, P.49, D.71 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.71 PEG.22: 5 residues within 4Å: Chain C: H.44, G.47, I.48, P.49, D.71 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.47 PEG.38: 5 residues within 4Å: Chain E: H.44, G.47, I.48, P.49, D.71 2 PLIP interactions: 2 interactions with chain E Water bridges: E:G.47, E:D.71 PEG.39: 6 residues within 4Å: Chain E: Y.72, F.74, A.83, E.86, L.87, E.90 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:L.87 PEG.47: 5 residues within 4Å: Chain F: H.44, G.47, I.48, P.49, D.71 1 PLIP interactions: 1 interactions with chain F Water bridges: F:D.71 PEG.54: 5 residues within 4Å: Chain G: H.44, G.47, I.48, P.49, D.71 1 PLIP interactions: 1 interactions with chain G Water bridges: G:G.47

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 16 residues within 4Å: Chain A: D.17, K.31, G.139, G.140 Chain B: D.17, K.31 Chain C: D.17, K.31 Chain D: D.17, K.31, N.33, G.139, G.140, E.141 Ligands: CL.3, EDO.16 6 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:K.31, D:G.140, B:K.31, A:K.31, A:G.140, C:K.31 PG4.40: 16 residues within 4Å: Chain E: D.17, K.31, G.139, G.140 Chain F: D.17, K.31 Chain G: D.17, K.31 Chain H: D.17, K.31, N.33, G.139, G.140, E.141 Ligands: CL.35, EDO.48 6 PLIP interactions: 2 interactions with chain E, 1 interactions with chain G, 1 interactions with chain F, 2 interactions with chain H Hydrogen bonds: E:K.31, E:G.140, G:K.31, F:K.31, H:K.31, H:G.140

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

EDO.9: 6 residues within 4Å: Chain A: P.124, F.125, Y.126, R.128 Chain B: E.149 Chain F: F.134 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: L.156, F.159, I.160, I.163 Chain C: K.112 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: M.1, I.133, F.134, K.150 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: D.17 Chain B: D.17, K.31, N.33, G.139, G.140, E.141 Chain D: K.31 Ligands: PG4.8 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: A.65, E.66, K.67, K.69, V.70 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: K.112 Chain B: I.160, I.163, Q.164 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain C: K.5, L.6, G.47, I.48, P.49, L.91, I.93 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain C: E.59, R.62 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: F.41, V.162, I.163 Chain D: L.105, N.106 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain D: R.145, E.146, F.147, E.149, K.150 Ligands: EDO.32 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain B: P.124, F.125, Y.126 Chain D: K.137, R.145, E.146, E.149 Ligands: EDO.31 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: F.134 Chain E: P.124, F.125, Y.126, R.128 Chain F: E.149 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain E: L.156, F.159, I.160, I.163 Chain G: K.112 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain E: M.1, I.133, F.134, K.150 Ligand excluded by PLIP EDO.48: 9 residues within 4Å: Chain E: D.17 Chain F: D.17, K.31, N.33, G.139, G.140, E.141 Chain H: K.31 Ligands: PG4.40 Ligand excluded by PLIP EDO.49: 5 residues within 4Å: Chain F: A.65, E.66, K.67, K.69, V.70 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain E: K.112 Chain F: I.160, I.163, Q.164 Ligand excluded by PLIP EDO.55: 7 residues within 4Å: Chain G: K.5, L.6, G.47, I.48, P.49, L.91, I.93 Ligand excluded by PLIP EDO.56: 2 residues within 4Å: Chain G: E.59, R.62 Ligand excluded by PLIP EDO.62: 5 residues within 4Å: Chain G: F.41, V.162, I.163 Chain H: L.105, N.106 Ligand excluded by PLIP EDO.63: 6 residues within 4Å: Chain H: R.145, E.146, F.147, E.149, K.150 Ligands: EDO.64 Ligand excluded by PLIP EDO.64: 8 residues within 4Å: Chain F: P.124, F.125, Y.126 Chain H: K.137, R.145, E.146, E.149 Ligands: EDO.63 Ligand excluded by PLIP

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.29: 12 residues within 4Å: Chain B: Q.24 Chain C: R.63, K.67 Chain D: Y.22, D.23, T.25, G.26, N.27, E.28, E.56, K.57, T.58 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.23, D:G.26, D:N.27, D:K.57 Water bridges: D:K.57 PGE.61: 12 residues within 4Å: Chain F: Q.24 Chain G: R.63, K.67 Chain H: Y.22, D.23, T.25, G.26, N.27, E.28, E.56, K.57, T.58 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:D.23, H:G.26, H:N.27, H:K.57 Water bridges: H:K.57

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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