SMTL ID : 2dwc.2 (1 other biounit)

Crystal structure of Probable phosphoribosylglycinamide formyl transferase from Pyrococcus horikoshii OT3 complexed with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: R.414, W.420 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.420 Water bridges: A:R.358, A:R.360, A:R.360, A:R.414 Salt bridges: A:R.414 SO4.2: 3 residues within 4Å: Chain A: K.378, Y.382, R.385 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.382 Water bridges: A:Y.51, A:K.378, A:K.378, A:K.378, A:K.378 Salt bridges: A:K.378, A:R.385 SO4.4: 3 residues within 4Å: Chain B: K.378, Y.382, R.385 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.382 Water bridges: B:Y.51, B:Y.51, B:K.378, B:K.378, B:K.378, B:K.378 Salt bridges: B:K.378, B:R.385 SO4.5: 2 residues within 4Å: Chain B: R.414, W.420 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.420 Water bridges: B:R.358, B:R.360 Salt bridges: B:R.414 SO4.7: 2 residues within 4Å: Chain C: R.414, W.420 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.420 Water bridges: C:R.358, C:R.360, C:R.414 Salt bridges: C:R.414 SO4.8: 3 residues within 4Å: Chain C: K.378, Y.382, R.385 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Y.382, C:Y.382 Water bridges: C:Y.51, C:Y.51, C:K.378, C:K.378, C:K.378, C:K.378 Salt bridges: C:K.378, C:R.385 SO4.10: 3 residues within 4Å: Chain D: K.378, Y.382, R.385 6 PLIP interactions: 6 interactions with chain D Water bridges: D:K.378, D:K.378, D:K.378, D:K.378 Salt bridges: D:K.378, D:R.385 SO4.11: 2 residues within 4Å: Chain D: R.414, W.420 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.420 Water bridges: D:R.358, D:R.360 Salt bridges: D:R.414

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 14 residues within 4Å: Chain A: R.121, S.137, H.160, K.162, E.202, E.203, H.204, I.205, F.207, E.210, Q.237, F.281, N.290, E.291 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.137, A:K.162, A:E.202, A:I.205, A:E.210, A:N.290, A:E.291 Water bridges: A:R.121, A:R.121 Salt bridges: A:R.121, A:R.121, A:K.162 pi-Stacking: A:H.160, A:H.160 ADP.6: 14 residues within 4Å: Chain B: R.121, S.137, H.160, K.162, E.202, E.203, H.204, I.205, F.207, E.210, Q.237, F.281, N.290, E.291 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.137, B:K.162, B:E.202, B:E.202, B:I.205, B:E.210, B:N.290, B:E.291 Water bridges: B:R.121 Salt bridges: B:R.121, B:R.121, B:K.162 pi-Stacking: B:H.160, B:H.160 ADP.9: 14 residues within 4Å: Chain C: R.121, S.137, H.160, K.162, E.202, E.203, H.204, I.205, F.207, E.210, Q.237, F.281, N.290, E.291 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:S.137, C:K.162, C:E.202, C:E.202, C:H.204, C:I.205, C:E.210, C:N.290, C:E.291 Water bridges: C:R.121, C:R.121 Salt bridges: C:R.121, C:R.121, C:K.162 pi-Stacking: C:H.160, C:H.160 ADP.12: 14 residues within 4Å: Chain D: R.121, S.137, H.160, K.162, E.202, E.203, H.204, I.205, F.207, E.210, Q.237, F.281, N.290, E.291 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.137, D:K.162, D:E.202, D:H.204, D:I.205, D:E.210, D:N.290, D:E.291 Water bridges: D:R.121, D:E.210 Salt bridges: D:R.121, D:R.121, D:K.162 pi-Stacking: D:H.160, D:H.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshikawa, S. et al., Crystal structure of Probable phosphoribosylglycinamide formyl transferase from Pyrococcus horikoshii OT3 complexed with ADP. To be Published

Release Date

2007-02-10

Peptides

433aa long hypothetical phosphoribosylglycinamide formyl transferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

433aa long hypothetical phosphoribosylglycinamide formyl transferase

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