SMTL ID : 3e2d.1

The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.273, H.277, H.316, H.465 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.273, A:D.273, A:H.277, A:H.465 ZN.2: 7 residues within 4Å: Chain A: D.12, S.65, D.273, D.315, H.316, H.465 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.12, A:D.12, A:S.65, A:D.315, A:H.316 ZN.13: 4 residues within 4Å: Chain B: D.273, H.277, H.465 Ligands: SO4.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.273, B:D.273, B:H.277, B:H.465 ZN.14: 6 residues within 4Å: Chain B: D.12, S.65, D.273, D.315, H.316 Ligands: SO4.16 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.12, B:D.12, B:S.65, B:D.315, B:H.316

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.12, S.65, T.118, E.268 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.12, A:T.118, A:E.268, H2O.1, H2O.1, H2O.3 MG.15: 4 residues within 4Å: Chain B: D.12, S.65, T.118, E.268 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.12, B:T.118, B:E.268, H2O.17, H2O.18, H2O.18

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 12 residues within 4Å: Chain A: D.12, D.64, S.65, H.116, R.129, D.273, H.277, D.315, H.316, H.465 Ligands: ZN.1, ZN.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.65, A:S.65 Water bridges: A:H.116, B:Y.325 Salt bridges: A:R.129, A:H.316, A:H.465 SO4.5: 5 residues within 4Å: Chain A: V.178, Y.179, A.221, Y.222, Q.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.179, A:Y.222 Water bridges: A:D.177, A:S.223, A:G.224 SO4.6: 6 residues within 4Å: Chain A: S.130, L.131, E.132, N.133, Q.134, K.185 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.133, A:N.133, A:Q.134, A:Q.134 Water bridges: A:K.185 Salt bridges: A:K.185 SO4.7: 3 residues within 4Å: Chain A: K.212, K.251, N.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.254 Salt bridges: A:K.212, A:K.251 SO4.8: 5 residues within 4Å: Chain A: K.235, K.236, S.237, G.238, R.240 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.205, A:K.236, A:G.238 Water bridges: A:R.205 Salt bridges: A:R.240 SO4.9: 2 residues within 4Å: Chain A: Q.376, R.444 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.376 Water bridges: A:S.411 Salt bridges: A:R.444 SO4.16: 12 residues within 4Å: Chain B: D.12, D.64, S.65, H.116, R.129, D.273, H.277, D.315, H.316, H.465 Ligands: ZN.13, ZN.14 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.65, B:S.65, B:S.65, B:D.273 Water bridges: B:A.117, B:R.129, B:D.273, B:D.273 Salt bridges: B:R.129, B:H.316, B:H.465 SO4.17: 5 residues within 4Å: Chain B: V.178, Y.179, A.221, Y.222, Q.242 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.179, B:Y.222, B:Q.242 Water bridges: B:S.223 SO4.18: 5 residues within 4Å: Chain B: S.130, L.131, E.132, N.133, Q.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.133, B:N.133, B:Q.134, B:Q.134 SO4.19: 4 residues within 4Å: Chain B: A.211, K.212, K.251, N.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.254 Salt bridges: B:K.212, B:K.251 SO4.20: 2 residues within 4Å: Chain B: Q.376, R.444 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.376 Water bridges: B:R.444, B:R.444, B:R.444 Salt bridges: B:R.444

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

EDO.10: 6 residues within 4Å: Chain A: P.331, N.351, G.353, A.354 Chain B: D.59, A.60 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.59, A:N.351 Water bridges: A:F.352, A:F.355 EDO.11: 3 residues within 4Å: Chain A: W.274, H.277, Y.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.441 Water bridges: A:W.274 EDO.12: 6 residues within 4Å: Chain A: D.59, A.60 Chain B: P.331, N.351, G.353, A.354 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.59, B:N.351 Water bridges: B:F.352, B:F.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Helland, R. et al., The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase. Biochim.Biophys.Acta (2009)

Release Date

2009-06-16

Peptides

Alkaline phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alkaline phosphatase