SMTL ID : 3r5v.1 (1 other biounit)

The structure of calcium bound Thermococcus thioreducens inorganic pyrophosphatase at 298K

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-hexamer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.1, H2O.2 CA.4: 3 residues within 4Å: Chain B: D.66, D.71, D.103 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.66, B:D.71, B:D.103, H2O.5, H2O.6, H2O.8 CA.5: 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.10, H2O.11 CA.6: 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.9: 3 residues within 4Å: Chain E: D.66, D.71, D.103 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.66, E:D.71, E:D.103, H2O.17, H2O.18, H2O.19 CA.10: 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.22, H2O.23

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

MRD.2: 6 residues within 4Å: Chain B: R.77, Y.115 Chain F: R.77, Y.115, F.116 Ligands: MPD.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:Y.115, F:F.116 Water bridges: B:K.25 MRD.7: 6 residues within 4Å: Chain C: R.77, Y.115, F.116 Chain E: R.77, Y.115 Ligands: MPD.8 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:Y.115, C:F.116 Water bridges: E:K.25

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

MPD.3: 6 residues within 4Å: Chain B: Y.115 Chain F: I.75, Y.115, F.116, F.129 Ligands: MRD.2 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:I.75, F:Y.115, F:F.116, B:Y.115 Water bridges: F:K.25 MPD.8: 6 residues within 4Å: Chain C: I.75, Y.115, F.116, F.129 Chain E: Y.115 Ligands: MRD.7 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain C Hydrophobic interactions: E:Y.115, C:I.75, C:Y.115, C:F.116 Water bridges: C:K.25

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Hughes, R.C. et al., The structure of calcium bound Thermococcus thioreducens inorganic pyrophosphatase at 298K. To be Published

Release Date

2012-03-28

Peptides

Tt-IPPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
A

E
C

F
E

Tt-IPPase

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