SMTL ID : 3i98.1 (1 other biounit)

X-ray crystallographic structure of Inorganic Pyrophosphatase at 298K from archaeon Thermococcus thioreducens

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 5 residues within 4Å: Chain A: Y.115, F.116 Chain D: Y.115, F.116 Ligands: MRD.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.116, D:F.116 Water bridges: D:R.77 MRD.7: 5 residues within 4Å: Chain A: Y.115, F.116 Chain D: Y.115, F.116 Ligands: MRD.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.116, D:F.116 Hydrogen bonds: A:Y.115 Water bridges: A:R.77

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.66, D.71, D.103 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.66, A:D.71, A:D.103, H2O.2, H2O.2 CA.4: 3 residues within 4Å: Chain B: D.66, D.71, D.103 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.66, B:D.71, B:D.103, H2O.5, H2O.7 CA.6: 3 residues within 4Å: Chain C: D.66, D.71, D.103 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.66, C:D.71, C:D.103, H2O.9, H2O.11 CA.8: 3 residues within 4Å: Chain D: D.66, D.71, D.103 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.66, D:D.71, D:D.103, H2O.13, H2O.14 CA.10: 3 residues within 4Å: Chain E: D.66, D.71, D.103 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.66, E:D.71, E:D.103, H2O.17, H2O.19 CA.12: 3 residues within 4Å: Chain F: D.66, D.71, D.103 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.66, F:D.71, F:D.103, H2O.21, H2O.23

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

MPD.3: 6 residues within 4Å: Chain B: R.77, Y.115 Chain F: I.75, R.77, Y.115, F.129 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:I.75, F:Y.115, F:F.129, B:Y.115 Water bridges: B:R.77, B:R.77 MPD.9: 6 residues within 4Å: Chain C: I.75, R.77, Y.115, F.129 Chain E: R.77, Y.115 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:Y.115, C:I.75, C:Y.115, C:F.129 Water bridges: E:R.77, E:R.77

2 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.5: 4 residues within 4Å: Chain C: A.128, D.131 Chain E: P.114 Chain F: Y.47 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:P.114, F:Y.47 ACE.11: 4 residues within 4Å: Chain B: P.114 Chain C: Y.47 Chain F: A.128, D.131 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: F:D.131 Hydrophobic interactions: C:Y.47, B:P.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hughes, R.C. et al., X-ray crystallographic structure of Inorganic Pyrophosphatase at 298K from archaeon Thermococcus thioreducens. To be Published

Release Date

2009-08-18

Peptides

Th-IPP: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
A

E
C

F
E

Th-IPP

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