SMTL ID : 2czg.1

Crystal structure of Probable phosphoribosylglycinamide formyl transferase (PH0318) from Pyrococcus horikoshii OT3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.378, Y.382, R.385 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.382 Water bridges: A:R.385 Salt bridges: A:K.378, A:R.385 SO4.2: 2 residues within 4Å: Chain A: R.414, W.420 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.360, A:R.360 Salt bridges: A:R.414 SO4.9: 3 residues within 4Å: Chain B: K.378, Y.382, R.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.382 Salt bridges: B:K.378, B:R.385 SO4.10: 2 residues within 4Å: Chain B: R.414, W.420 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.420 Water bridges: B:R.358 Salt bridges: B:R.414 SO4.11: 5 residues within 4Å: Chain B: H.120, R.121, E.122, R.123, I.164 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.121, B:E.122, B:R.123 Salt bridges: B:R.123 SO4.12: 4 residues within 4Å: Chain B: R.121, K.162, N.290, E.291 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.290, B:E.291 Salt bridges: B:R.121, B:K.162

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain A: E.37, T.303, L.304, H.307, P.308, P.309, G.310, F.311, S.312, A.315 Ligands: GOL.13 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.307, A:G.310 Water bridges: A:L.304, B:R.40, B:R.40 GOL.4: 6 residues within 4Å: Chain A: N.370, W.393 Chain B: P.308, P.327, F.337, P.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.370, A:N.370 Water bridges: A:N.370 GOL.5: 4 residues within 4Å: Chain A: D.220, E.221, W.330, R.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.221, A:E.221, A:R.335 Water bridges: A:N.222 GOL.6: 4 residues within 4Å: Chain A: I.225, V.226, T.227, K.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.227, A:T.227, A:K.264 Water bridges: A:I.225, A:T.227 GOL.7: 4 residues within 4Å: Chain A: R.358 Chain B: E.10, S.18, Q.20 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.18, B:Q.20, A:R.358, A:R.358 Water bridges: B:D.17, B:D.17 GOL.8: 5 residues within 4Å: Chain A: R.62, S.63, Y.64, R.80, E.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.80 Water bridges: A:S.63 GOL.13: 5 residues within 4Å: Chain A: R.40 Chain B: R.40, P.309, G.310 Ligands: GOL.3 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.40, B:R.40, B:G.310, A:R.40 Water bridges: B:E.37, B:E.37, B:F.311, B:F.311 GOL.14: 7 residues within 4Å: Chain A: P.308, P.327, F.337, P.338 Chain B: P.369, N.370, W.393 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.370, B:N.370, B:W.393 GOL.15: 8 residues within 4Å: Chain B: V.226, T.227, F.229, K.264, W.330, G.333, Y.334, R.335 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.227, B:K.264, B:R.335 GOL.16: 5 residues within 4Å: Chain B: R.62, S.63, Y.64, R.80, E.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.63, B:R.80, B:E.81 Water bridges: B:S.63 GOL.17: 5 residues within 4Å: Chain A: N.53, Q.58 Chain B: T.15, H.61, R.62 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.62, A:N.53 Water bridges: B:A.60, A:Q.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshikawa, S. et al., Crystal structure of Probable phosphoribosylglycinamide formyl transferase (PH0318) from Pyrococcus horikoshii OT3. To be Published

Release Date

2006-01-13

Peptides

phosphoribosylglycinamide formyl transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

phosphoribosylglycinamide formyl transferase

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