SMTL ID : 3o3l.1

Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol (1,3,4,5)tetrakisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: Y.36, R.304, E.305, A.340 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.340 Hydrogen bonds: A:Y.36, A:Y.36 Salt bridges: A:R.304 ACT.2: 5 residues within 4Å: Chain A: D.44 Chain B: T.173, V.190, R.191, R.192 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.190 Hydrogen bonds: B:T.173 Water bridges: B:R.192 ACT.3: 6 residues within 4Å: Chain A: H.218, K.299, Y.302, Y.303, K.306 Ligands: 4IP.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.299, A:Y.302, A:Y.303 Water bridges: A:K.306 Salt bridges: A:H.218, A:K.299, A:K.306 ACT.10: 4 residues within 4Å: Chain B: Y.36, R.304, E.305, A.340 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.36, B:A.340 Hydrogen bonds: B:Y.36 Salt bridges: B:R.304 ACT.11: 6 residues within 4Å: Chain B: H.218, K.299, Y.302, Y.303, K.306 Ligands: 4IP.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.299, B:Y.302, B:Y.303 Water bridges: B:H.218, B:K.306 Salt bridges: B:H.218, B:K.299, B:K.306

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: A.111, A.112, R.115, A.206, G.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.115, A:G.207 GOL.5: 6 residues within 4Å: Chain A: K.77, F.283, F.288, I.290, K.291, Y.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.77, A:K.291 Water bridges: A:K.77, A:K.77, A:K.77 GOL.6: 5 residues within 4Å: Chain A: Y.233, P.237, Q.238, A.240, K.264 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.233, A:Q.238 Water bridges: A:L.94, A:H.95, A:A.240, A:K.264, A:K.264 GOL.7: 4 residues within 4Å: Chain A: D.53, N.54, D.55, R.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.53, A:D.55, A:D.55, A:R.62, A:S.100 GOL.12: 5 residues within 4Å: Chain B: K.77, F.283, F.288, K.291, Y.303 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.77, B:K.291 Water bridges: B:K.77, B:Y.303, B:Y.303 GOL.13: 4 residues within 4Å: Chain B: A.111, A.112, R.115, G.207 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.111, B:R.115, B:G.207 GOL.14: 5 residues within 4Å: Chain B: D.53, N.54, D.55, R.62, S.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.55, B:D.55, B:R.62, B:S.100, B:S.100 GOL.15: 6 residues within 4Å: Chain B: L.94, Y.233, P.237, Q.238, A.240, K.264 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.94, B:Y.233, B:Q.238 Water bridges: B:H.95, B:K.264, B:K.264

2 x 4IP: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE(Non-covalent)

4IP.8: 15 residues within 4Å: Chain A: R.51, D.147, K.183, D.217, H.218, S.246, E.247, A.248, G.249, V.250, G.251, R.252, K.299, Y.303 Ligands: ACT.3 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:D.217, A:S.246, A:E.247, A:A.248, A:G.249, A:V.250, A:G.251, A:R.252 Water bridges: A:R.51, A:R.51, A:R.62, A:Y.143, A:R.146, A:K.183, A:K.183, A:H.218, A:K.299, A:Y.303, A:K.306, A:K.306 Salt bridges: A:R.51, A:K.183, A:K.183, A:H.218, A:H.218, A:H.218, A:R.252, A:K.299, A:K.299 4IP.16: 15 residues within 4Å: Chain B: R.51, D.147, K.183, D.217, H.218, S.246, E.247, A.248, G.249, V.250, G.251, R.252, K.299, Y.303 Ligands: ACT.11 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:D.217, B:S.246, B:E.247, B:A.248, B:G.249, B:V.250, B:G.251, B:R.252 Water bridges: B:R.51, B:R.51, B:R.51, B:R.51, B:K.183, B:H.218, B:H.218, B:Y.303, B:K.306 Salt bridges: B:R.51, B:K.183, B:K.183, B:H.218, B:H.218, B:H.218, B:R.252, B:K.299, B:K.299

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

CL.9: 2 residues within 4Å: Chain A: S.154, Q.155 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gruninger, R.J. et al., Structural analysis of substrate binding in PTPLPs. To be Published

Release Date

2011-12-07

Peptides

Myo-inositol hexaphosphate phosphohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Myo-inositol hexaphosphate phosphohydrolase