SMTL ID : 2vqr.1

Crystal structure of a phosphonate monoester hydrolase from rhizobium leguminosarum: a new member of the alkaline phosphatase superfamily

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.41, A.86, D.353, H.354 Ligands: CA.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.41, A:D.41, A:D.353, A:H.354 MN.6: 5 residues within 4Å: Chain B: D.41, A.86, D.353, H.354 Ligands: CA.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.41, B:D.41, B:D.353, B:H.354 MN.11: 5 residues within 4Å: Chain C: D.41, A.86, D.353, H.354 Ligands: CA.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.41, C:D.41, C:D.353, C:H.354 MN.16: 5 residues within 4Å: Chain D: D.41, A.86, D.353, H.354 Ligands: CA.17 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.41, D:D.41, D:D.353, D:H.354

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.41, A.86, D.353, H.354 Ligands: MN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.41, A:D.41, A:D.353, A:H.354 CA.7: 5 residues within 4Å: Chain B: D.41, A.86, D.353, H.354 Ligands: MN.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.41, B:D.41, B:D.353, B:H.354 CA.12: 5 residues within 4Å: Chain C: D.41, A.86, D.353, H.354 Ligands: MN.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.41, C:D.41, C:D.353, C:H.354 CA.17: 5 residues within 4Å: Chain D: D.41, A.86, D.353, H.354 Ligands: MN.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.41, D:D.41, D:D.353, D:H.354

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

ACT.3: 4 residues within 4Å: Chain A: R.473, Y.474, D.488, R.490 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.473 Hydrogen bonds: A:R.490 Water bridges: A:Y.474 Salt bridges: A:H.491 ACT.5: 8 residues within 4Å: Chain A: Y.134, T.135, T.136, G.155, D.156, L.157, E.168, P.169 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.134 Hydrogen bonds: A:T.135, A:T.136, A:G.155 ACT.8: 4 residues within 4Å: Chain B: R.473, Y.474, D.488, R.490 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.473 Hydrogen bonds: B:R.490 Salt bridges: B:H.491 ACT.10: 8 residues within 4Å: Chain B: Y.134, T.135, T.136, G.155, D.156, L.157, E.168, P.169 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.134 Hydrogen bonds: B:T.135, B:T.136, B:G.155 ACT.13: 4 residues within 4Å: Chain C: R.473, Y.474, D.488, R.490 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:R.473 Hydrogen bonds: C:R.490 Water bridges: C:Y.474 Salt bridges: C:H.491 ACT.15: 8 residues within 4Å: Chain C: Y.134, T.135, T.136, G.155, D.156, L.157, E.168, P.169 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.134 Hydrogen bonds: C:T.135, C:T.136, C:G.155 ACT.18: 4 residues within 4Å: Chain D: R.473, Y.474, D.488, R.490 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:R.473 Hydrogen bonds: D:R.490 Salt bridges: D:H.491 ACT.20: 8 residues within 4Å: Chain D: Y.134, T.135, T.136, G.155, D.156, L.157, E.168, P.169 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.134 Hydrogen bonds: D:T.135, D:T.136, D:G.155

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jonas, S. et al., A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium Leguminosarum. J.Mol.Biol. (2008)

Release Date

2008-09-30

Peptides

PUTATIVE SULFATASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

PUTATIVE SULFATASE