SMTL ID : 2o2r.1 (1 other biounit)

Crystal structure of the C-terminal domain of rat 10'formyltetrahydrofolate dehydrogenase in complex with NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.169 Chain C: K.467 Ligand excluded by PLIP SO4.2: 2 residues within 4Å: Chain A: R.251, P.256 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: R.379, Y.414 Ligand excluded by PLIP SO4.4: 8 residues within 4Å: Chain A: K.284, L.508, R.509, I.510 Chain B: F.490, F.495, G.496, K.497 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: R.166, R.169 Chain C: Y.463, K.467 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: R.169 Chain D: D.466, K.467 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain B: R.251, P.256 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain B: R.379, Y.414 Ligand excluded by PLIP SO4.11: 8 residues within 4Å: Chain A: F.490, F.495, G.496, K.497 Chain B: K.284, L.508, R.509, I.510 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: R.166, R.169 Chain D: Y.463, K.467 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: K.467 Chain C: R.169 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain C: R.251, P.256 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain C: R.379, Y.414 Ligand excluded by PLIP SO4.18: 8 residues within 4Å: Chain C: K.284, L.508, R.509, I.510 Chain D: F.490, F.495, G.496, K.497 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: K.30, R.357 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain A: Y.463, K.467 Chain C: R.166, P.167, R.169 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: D.466, K.467 Chain D: R.169 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain D: R.251, P.256 Ligand excluded by PLIP SO4.25: 1 residues within 4Å: Chain D: R.379 Ligand excluded by PLIP SO4.26: 8 residues within 4Å: Chain C: F.490, F.495, G.496, K.497 Chain D: K.284, L.508, R.509, I.510 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain B: Y.463 Chain D: R.166, R.169 Ligand excluded by PLIP

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.6: 19 residues within 4Å: Chain A: V.185, I.186, P.187, W.188, K.212, A.214, Q.215, S.244, G.245, S.246, G.249, Q.250, F.263, T.264, G.265, S.266, V.269, H.272, I.273 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.186, A:K.212, A:Q.215, A:G.245, A:Q.250, A:S.266 Water bridges: A:W.188, A:V.216, A:S.246 Salt bridges: A:K.212 NDP.13: 17 residues within 4Å: Chain B: V.185, I.186, W.188, K.212, A.214, Q.215, S.244, G.245, G.249, Q.250, F.263, T.264, G.265, S.266, V.269, H.272, I.273 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:I.186, B:W.188, B:K.212, B:Q.215, B:G.245, B:Q.250, B:S.266 Water bridges: B:V.216, B:S.246 Salt bridges: B:K.212 NDP.21: 18 residues within 4Å: Chain C: V.185, I.186, W.188, K.212, A.214, Q.215, S.244, G.245, S.246, G.249, Q.250, F.263, T.264, G.265, S.266, V.269, H.272, I.273 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:I.186, C:K.212, C:Q.215, C:G.245, C:Q.250, C:S.266, C:S.266 Water bridges: C:V.216, C:S.246 Salt bridges: C:K.212 NDP.28: 18 residues within 4Å: Chain D: V.185, I.186, W.188, K.212, A.214, Q.215, S.244, G.245, S.246, G.249, Q.250, F.263, T.264, G.265, S.266, V.269, H.272, I.273 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:I.186, D:K.212, D:Q.215, D:G.245, D:Q.250, D:S.266 Water bridges: D:V.216, D:S.246, D:S.246, D:S.276 Salt bridges: D:K.212

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: T.136, Y.190, M.193, W.197, N.321, I.323, N.479, T.481 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.190, A:Y.190, A:N.321, A:T.481 GOL.14: 8 residues within 4Å: Chain B: Y.190, M.193, W.197, F.316, N.321, I.323, N.479, T.481 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.321, B:N.479, B:T.481 GOL.22: 7 residues within 4Å: Chain C: Y.190, M.193, W.197, N.321, I.323, N.479, T.481 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.321, C:N.479 Water bridges: C:N.479, C:T.481 GOL.29: 8 residues within 4Å: Chain D: Y.190, M.193, W.197, F.316, N.321, I.323, N.479, T.481 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.321, D:N.321 Water bridges: D:N.479, D:T.481

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsybovsky, Y. et al., Crystal structures of the carboxyl terminal domain of rat 10-formyltetrahydrofolate dehydrogenase: implications for the catalytic mechanism of aldehyde dehydrogenases. Biochemistry (2007)

Release Date

2007-03-06

Peptides

Formyltetrahydrofolate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Formyltetrahydrofolate dehydrogenase

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