SMTL ID : 4iok.1

N10-formyltetrahydrofolate synthetase from Moorella thermoacetica with ADP, XPO

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.175, R.178, G.537 Chain B: A.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.537 Water bridges: A:R.178 Salt bridges: A:R.175, A:R.178 SO4.7: 4 residues within 4Å: Chain A: A.188 Chain B: R.175, R.178, G.537 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.537, A:A.188 Salt bridges: B:R.175, B:R.178 SO4.12: 4 residues within 4Å: Chain C: R.175, R.178, G.537 Chain D: A.188 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.537 Water bridges: C:R.178 Salt bridges: C:R.175, C:R.178 SO4.18: 4 residues within 4Å: Chain C: A.188 Chain D: R.175, R.178, G.537 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.537, C:A.188 Salt bridges: D:R.175, D:R.178

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

ADP.2: 19 residues within 4Å: Chain A: D.7, A.70, G.71, E.72, G.73, K.74, T.75, T.76, K.108, G.113, G.114, E.301, N.382, A.383, F.384, P.385, W.412 Ligands: XPO.3, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:E.72, A:G.73, A:K.74, A:T.75, A:T.76, A:T.76, A:G.113, A:N.382, A:A.383 Water bridges: A:T.75, A:R.97, A:W.412 Salt bridges: A:K.74, A:K.108, A:K.108 pi-Stacking: A:F.384, A:W.412 ADP.8: 19 residues within 4Å: Chain B: D.7, A.70, G.71, E.72, G.73, K.74, T.75, T.76, K.108, G.113, G.114, E.301, N.382, A.383, F.384, P.385, W.412 Ligands: XPO.9, MG.10 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:E.72, B:G.73, B:K.74, B:T.75, B:T.75, B:T.76, B:T.76, B:G.113, B:N.382, B:A.383 Water bridges: B:K.108, B:E.301, B:W.412 Salt bridges: B:K.74, B:K.108, B:K.108 pi-Stacking: B:F.384, B:W.412 ADP.13: 19 residues within 4Å: Chain C: D.7, A.70, G.71, E.72, G.73, K.74, T.75, T.76, K.108, G.113, G.114, E.301, N.382, A.383, F.384, P.385, W.412 Ligands: XPO.14, MG.15 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:E.72, C:G.73, C:K.74, C:T.75, C:T.76, C:T.76, C:G.113, C:N.382, C:A.383 Water bridges: C:T.75, C:R.97, C:W.412 Salt bridges: C:K.74, C:K.108, C:K.108 pi-Stacking: C:F.384, C:W.412 ADP.19: 19 residues within 4Å: Chain D: D.7, A.70, G.71, E.72, G.73, K.74, T.75, T.76, K.108, G.113, G.114, E.301, N.382, A.383, F.384, P.385, W.412 Ligands: XPO.20, MG.21 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:E.72, D:G.73, D:K.74, D:T.75, D:T.75, D:T.76, D:T.76, D:G.113, D:N.382, D:A.383 Water bridges: D:K.108, D:E.301, D:W.412 Salt bridges: D:K.74, D:K.108, D:K.108 pi-Stacking: D:F.384, D:W.412

4 x XPO: FORMYL PHOSPHATE(Non-covalent)

XPO.3: 10 residues within 4Å: Chain A: P.67, G.71, K.74, R.97, K.108, E.301, G.303, F.304 Ligands: ADP.2, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.72, A:K.74, A:F.304 Water bridges: A:T.75, A:T.75, A:R.97, A:R.97 Salt bridges: A:K.74, A:R.97, A:K.108 XPO.9: 10 residues within 4Å: Chain B: P.67, G.71, K.74, R.97, K.108, E.301, G.303, F.304 Ligands: ADP.8, MG.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.304 Water bridges: B:R.97, B:R.97 Salt bridges: B:K.74, B:R.97, B:K.108 XPO.14: 10 residues within 4Å: Chain C: P.67, G.71, K.74, R.97, K.108, E.301, G.303, F.304 Ligands: ADP.13, MG.15 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.72, C:K.74, C:F.304 Water bridges: C:T.75, C:T.75, C:R.97, C:R.97 Salt bridges: C:K.74, C:R.97, C:K.108 XPO.20: 10 residues within 4Å: Chain D: P.67, G.71, K.74, R.97, K.108, E.301, G.303, F.304 Ligands: ADP.19, MG.21 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:F.304 Water bridges: D:R.97, D:R.97 Salt bridges: D:K.74, D:R.97, D:K.108

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: K.74, T.75, E.301 Ligands: ADP.2, XPO.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.75, A:E.301, H2O.18, H2O.84 MG.10: 5 residues within 4Å: Chain B: T.75, R.97, E.301 Ligands: ADP.8, XPO.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.75, B:E.301, H2O.212, H2O.213 MG.15: 5 residues within 4Å: Chain C: K.74, T.75, E.301 Ligands: ADP.13, XPO.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.75, C:E.301, H2O.278, H2O.344 MG.21: 5 residues within 4Å: Chain D: T.75, R.97, E.301 Ligands: ADP.19, XPO.20 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.75, D:E.301, H2O.472, H2O.473

6 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.5: 4 residues within 4Å: Chain A: R.162, I.164, E.194 Chain C: G.185 No protein-ligand interaction detected (PLIP) TOE.6: 1 residues within 4Å: Chain A: R.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.87 TOE.11: 4 residues within 4Å: Chain B: R.162, I.164, E.194, E.515 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.194 TOE.16: 4 residues within 4Å: Chain A: G.185 Chain C: R.162, I.164, E.194 No protein-ligand interaction detected (PLIP) TOE.17: 1 residues within 4Å: Chain C: R.87 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.87 TOE.22: 4 residues within 4Å: Chain D: R.162, I.164, E.194, E.515 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stec, B., Time passes yet errors remain: Comments on the structure of N(10) -formyltetrahydrofolate synthetase. Protein Sci. (2013)

Release Date

2013-04-10

Peptides

Formate--tetrahydrofolate ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Formate--tetrahydrofolate ligase

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