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

Crystal structure of a HD-domain phosphohydrolase (lin2634) from LISTERIA INNOCUA at 1.98 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-hexamer

Ligands

22 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: R.19, H.34, H.68, D.69, K.79, D.138 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.34, A:H.68, A:D.69, A:D.138, H2O.5 CA.2: 3 residues within 4Å: Chain A: Y.18 Chain D: Y.18 Ligands: CA.15 No protein-ligand interaction detected (PLIP) CA.3: 2 residues within 4Å: Chain A: H.68, D.69 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.69, H2O.4, H2O.4, H2O.5, H2O.6 CA.4: 1 residues within 4Å: Chain A: D.51 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.51, H2O.5 CA.5: 1 residues within 4Å: Chain A: D.126 No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Chain A: E.185 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.185, H2O.2, H2O.4, H2O.5, H2O.6 CA.8: 6 residues within 4Å: Chain B: R.19, H.34, H.68, D.69, K.79, D.138 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.34, B:H.68, B:D.69, B:D.138, H2O.9 CA.9: 1 residues within 4Å: Chain C: Y.18 No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Chain B: H.68, D.69 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.68, B:D.69, H2O.8, H2O.9, H2O.9 CA.12: 5 residues within 4Å: Chain C: R.19, H.34, H.68, D.69, D.138 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.34, C:H.68, C:D.69, C:D.138, C:D.138 CA.13: 4 residues within 4Å: Chain C: H.68, D.69, S.71, E.72 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.68, C:D.69 CA.14: 6 residues within 4Å: Chain D: R.19, H.34, H.68, D.69, K.79, D.138 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.34, D:H.68, D:D.69, D:D.138, H2O.19 CA.15: 3 residues within 4Å: Chain A: Y.18 Chain D: Y.18 Ligands: CA.2 No protein-ligand interaction detected (PLIP) CA.16: 2 residues within 4Å: Chain D: H.68, D.69 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.69, H2O.18, H2O.19, H2O.20, H2O.20 CA.17: 1 residues within 4Å: Chain D: D.51 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.51, H2O.20 CA.18: 1 residues within 4Å: Chain D: D.126 No protein-ligand interaction detected (PLIP) CA.19: 1 residues within 4Å: Chain D: E.185 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.185, H2O.16, H2O.18, H2O.20, H2O.21 CA.21: 6 residues within 4Å: Chain E: R.19, H.34, H.68, D.69, K.79, D.138 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.34, E:H.68, E:D.69, E:D.138, H2O.23 CA.22: 1 residues within 4Å: Chain F: Y.18 No protein-ligand interaction detected (PLIP) CA.23: 2 residues within 4Å: Chain E: H.68, D.69 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.68, E:D.69, H2O.22, H2O.23, H2O.23 CA.25: 5 residues within 4Å: Chain F: R.19, H.34, H.68, D.69, D.138 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.34, F:H.68, F:D.69, F:D.138, F:D.138 CA.26: 4 residues within 4Å: Chain F: H.68, D.69, S.71, E.72 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.68, F:D.69

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 7 residues within 4Å: Chain A: I.75, G.76, D.77, I.78 Chain B: I.75, G.76, D.77 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.76, B:G.76 PEG.11: 4 residues within 4Å: Chain B: K.132, Y.173, E.175, M.176 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.132 Water bridges: B:Y.173 PEG.20: 7 residues within 4Å: Chain D: I.75, G.76, D.77, I.78 Chain E: I.75, G.76, D.77 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.76, D:G.76 PEG.24: 4 residues within 4Å: Chain E: K.132, Y.173, E.175, M.176 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.132 Water bridges: E:Y.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a HD-domain phosphohydrolase (lin2634) from LISTERIA INNOCUA at 1.98 A resolution. To be published

Release Date

2010-05-26

Peptides

Lin2634 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Lin2634 protein

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