SMTL ID : 3q3q.1

Crystal Structure of SPAP: an novel alkaline phosphatase from bacterium Sphingomonas sp. strain BSAR-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.49, T.89, K.171, D.300, D.345, H.346 Ligands: KOP.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.49, A:T.89, A:D.345, A:H.346 ZN.2: 5 residues within 4Å: Chain A: Q.50, D.300, H.304, H.491 Ligands: KOP.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.300, A:D.300, A:H.304, A:H.491 ZN.10: 7 residues within 4Å: Chain B: D.49, T.89, K.171, D.300, D.345, H.346 Ligands: KOP.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.49, B:T.89, B:D.345, B:H.346 ZN.11: 5 residues within 4Å: Chain B: Q.50, D.300, H.304, H.491 Ligands: KOP.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.300, B:D.300, B:H.304, B:H.491

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.547, V.549, G.551, D.553 Chain B: M.357 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.547, A:V.549, A:G.551, A:D.553, B:M.357, H2O.64 CA.12: 5 residues within 4Å: Chain A: M.357 Chain B: D.547, V.549, G.551, D.553 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.547, B:V.549, B:G.551, B:D.553, A:M.357, H2O.342

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: S.103, R.104, S.442, R.457, D.542 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.103, A:R.104, A:R.457, A:R.457, A:D.542 Water bridges: A:R.101 GOL.5: 10 residues within 4Å: Chain A: A.85, A.86, S.397, G.398, L.469, L.470, L.471, G.492, S.493, P.494 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.85, A:S.397, A:S.397 Water bridges: A:T.87, A:S.478 GOL.6: 5 residues within 4Å: Chain A: Q.511, A.550, G.551, K.552 Chain B: F.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.511, A:Q.511, A:K.552 Water bridges: A:D.553 GOL.7: 7 residues within 4Å: Chain A: W.450, L.452, E.455, P.494, W.495, D.496 Chain B: S.449 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.494 Water bridges: A:L.452, A:D.496, A:R.499, A:R.499, A:R.499, A:R.499, B:S.449, B:S.449 GOL.8: 5 residues within 4Å: Chain A: A.438, T.440, P.441, S.442, R.457 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.438, A:S.442, A:R.457 GOL.13: 5 residues within 4Å: Chain B: S.103, R.104, S.442, R.457, D.542 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.103, B:R.104, B:R.457, B:R.457, B:D.542 Water bridges: B:R.101 GOL.14: 10 residues within 4Å: Chain B: A.85, A.86, S.397, G.398, L.469, L.470, L.471, G.492, S.493, P.494 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.85, B:S.397, B:S.397 Water bridges: B:T.87, B:S.478 GOL.15: 5 residues within 4Å: Chain A: F.236 Chain B: Q.511, A.550, G.551, K.552 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.511, B:Q.511, B:K.552 Water bridges: B:D.553 GOL.16: 7 residues within 4Å: Chain A: S.449 Chain B: W.450, L.452, E.455, P.494, W.495, D.496 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.494 Water bridges: B:L.452, B:D.496, B:R.499, B:R.499, B:R.499, B:R.499, A:S.449, A:S.449 GOL.17: 5 residues within 4Å: Chain B: A.438, T.440, P.441, S.442, R.457 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.438, B:S.442, B:R.457

2 x KOP: METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

KOP.9: 12 residues within 4Å: Chain A: D.49, E.88, T.89, N.110, K.171, R.173, D.300, H.304, H.346, H.491 Ligands: ZN.1, ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.89, A:N.110 Salt bridges: A:K.171, A:R.173, A:H.304, A:H.346, A:H.491 KOP.18: 12 residues within 4Å: Chain B: D.49, E.88, T.89, N.110, K.171, R.173, D.300, H.304, H.346, H.491 Ligands: ZN.10, ZN.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.89, B:T.89, B:N.110, B:D.300 Salt bridges: B:K.171, B:R.173, B:H.304, B:H.346, B:H.491

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bihani, S.C. et al., X-ray structure reveals a new class and provides insight into evolution of alkaline phosphatases. Plos One (2011)

Release Date

2011-12-28

Peptides

Alkaline phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alkaline phosphatase