SMTL ID : 1wra.3 (2 other biounits)

Crystal Structure of Phosphorylcholine Esterase Domain of the Virulence Factor Choline Binding Protein E from Streptococcus Pneumoniae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: H.84, H.86, N.182, D.202 Ligands: FE.2, PC.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.84, A:H.86, A:D.202, H2O.1 FE.2: 6 residues within 4Å: Chain A: D.88, H.89, D.202, H.228 Ligands: FE.1, PC.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.88, A:H.89, A:D.202, A:H.228, H2O.1 FE.12: 6 residues within 4Å: Chain B: H.84, H.86, N.182, D.202 Ligands: FE.13, PC.16 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.84, B:H.86, B:D.202, H2O.8 FE.13: 6 residues within 4Å: Chain B: D.88, H.89, D.202, H.228 Ligands: FE.12, PC.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.88, B:H.89, B:D.202, B:H.228, H2O.8

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.36, G.91, D.94, E.95 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.36, A:D.94, A:E.95, H2O.1, H2O.1 CA.4: 3 residues within 4Å: Chain A: E.35, D.36, D.38 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.35, A:D.36, A:D.36, A:D.38, H2O.2 CA.14: 4 residues within 4Å: Chain B: D.36, G.91, D.94, E.95 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.36, B:D.94, B:E.95, H2O.9, H2O.9 CA.15: 3 residues within 4Å: Chain B: E.35, D.36, D.38 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.35, B:D.36, B:D.36, B:D.38, H2O.9

2 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.5: 11 residues within 4Å: Chain A: G.52, H.86, S.87, D.88, W.122, N.182, D.202, H.227, H.228 Ligands: FE.1, FE.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.182 Water bridges: A:R.120 Salt bridges: A:H.86, A:D.88, A:H.227 pi-Cation interactions: A:W.122 PC.16: 11 residues within 4Å: Chain B: G.52, H.86, S.87, D.88, W.122, N.182, D.202, H.227, H.228 Ligands: FE.12, FE.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.182 Water bridges: B:H.86, B:H.86, B:R.120 Salt bridges: B:H.86, B:D.88, B:H.227 pi-Cation interactions: B:W.122

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 3 residues within 4Å: Chain A: H.229, S.254, W.257 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.257, A:W.257 MPD.7: 3 residues within 4Å: Chain A: Q.75, T.99, Y.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.100 MPD.8: 2 residues within 4Å: Chain A: T.62, F.66 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.62 MPD.9: 5 residues within 4Å: Chain A: L.97, T.99, Y.100, P.101, T.138 No protein-ligand interaction detected (PLIP) MPD.10: 4 residues within 4Å: Chain A: D.41, W.49 Chain B: Y.37 Ligands: MPD.22 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.49, B:Y.37, B:Y.37 Hydrogen bonds: A:D.41 MPD.11: 5 residues within 4Å: Chain A: Y.37, Y.57 Chain B: D.41, W.49 Ligands: MPD.21 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.37, A:Y.57, B:W.49 MPD.17: 3 residues within 4Å: Chain B: H.229, S.254, W.257 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.257, B:W.257 MPD.18: 3 residues within 4Å: Chain B: Q.75, T.99, Y.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.100 Water bridges: B:Y.100 MPD.19: 2 residues within 4Å: Chain B: T.62, F.66 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.62 MPD.20: 5 residues within 4Å: Chain B: L.97, T.99, Y.100, P.101, T.138 No protein-ligand interaction detected (PLIP) MPD.21: 4 residues within 4Å: Chain A: Y.37 Chain B: D.41, W.49 Ligands: MPD.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.49, A:Y.37, A:Y.37 Hydrogen bonds: B:D.41 MPD.22: 5 residues within 4Å: Chain A: D.41, W.49 Chain B: Y.37, Y.57 Ligands: MPD.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.49, B:Y.37, B:Y.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garau, G. et al., Crystal structure of phosphorylcholine esterase domain of the virulence factor choline-binding protein e from streptococcus pneumoniae: new structural features among the metallo-beta-lactamase superfamily. J.Biol.Chem. (2005)

Release Date

2005-05-31

Peptides

Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Teichoic acid phosphorylcholine esterase/choline binding protein E (cbpE)

Related Entries With Identical Sequence