SMTL ID : 2o2r.2 (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-octamer

Ligands

42 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: 4 residues within 4Å: Chain C: K.30, R.357 Chain E: L.31, T.32 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 SO4.30: 2 residues within 4Å: Chain E: R.169 Chain G: K.467 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain E: R.251, P.256 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain E: R.379, Y.414 Ligand excluded by PLIP SO4.33: 8 residues within 4Å: Chain E: K.284, L.508, R.509, I.510 Chain F: F.490, F.495, G.496, K.497 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain E: R.166, R.169 Chain G: Y.463, K.467 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain F: R.169 Chain H: D.466, K.467 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain F: R.251, P.256 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain F: R.379, Y.414 Ligand excluded by PLIP SO4.40: 8 residues within 4Å: Chain E: F.490, F.495, G.496, K.497 Chain F: K.284, L.508, R.509, I.510 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain F: R.166, R.169 Chain H: Y.463, K.467 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain E: K.467 Chain G: R.169 Ligand excluded by PLIP SO4.45: 2 residues within 4Å: Chain G: R.251, P.256 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain G: R.379, Y.414 Ligand excluded by PLIP SO4.47: 8 residues within 4Å: Chain G: K.284, L.508, R.509, I.510 Chain H: F.490, F.495, G.496, K.497 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain A: L.31, T.32 Chain G: K.30, R.357 Ligand excluded by PLIP SO4.49: 5 residues within 4Å: Chain E: Y.463, K.467 Chain G: R.166, P.167, R.169 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain F: D.466, K.467 Chain H: R.169 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain H: R.251, P.256 Ligand excluded by PLIP SO4.54: 1 residues within 4Å: Chain H: R.379 Ligand excluded by PLIP SO4.55: 8 residues within 4Å: Chain G: F.490, F.495, G.496, K.497 Chain H: K.284, L.508, R.509, I.510 Ligand excluded by PLIP SO4.56: 3 residues within 4Å: Chain F: Y.463 Chain H: R.166, R.169 Ligand excluded by PLIP

8 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 NDP.35: 19 residues within 4Å: Chain E: 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 E Hydrogen bonds: E:I.186, E:K.212, E:Q.215, E:G.245, E:Q.250, E:S.266 Water bridges: E:W.188, E:V.216, E:S.246 Salt bridges: E:K.212 NDP.42: 17 residues within 4Å: Chain F: 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 F Hydrogen bonds: F:I.186, F:W.188, F:K.212, F:Q.215, F:G.245, F:Q.250, F:S.266 Water bridges: F:V.216, F:S.246 Salt bridges: F:K.212 NDP.50: 18 residues within 4Å: Chain G: 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 G Hydrogen bonds: G:I.186, G:K.212, G:Q.215, G:G.245, G:Q.250, G:S.266, G:S.266 Water bridges: G:V.216, G:S.246 Salt bridges: G:K.212 NDP.57: 18 residues within 4Å: Chain H: 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 H Hydrogen bonds: H:I.186, H:K.212, H:Q.215, H:G.245, H:Q.250, H:S.266 Water bridges: H:V.216, H:S.246, H:S.246, H:S.276 Salt bridges: H:K.212

8 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 GOL.36: 8 residues within 4Å: Chain E: T.136, Y.190, M.193, W.197, N.321, I.323, N.479, T.481 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.190, E:N.321 GOL.43: 8 residues within 4Å: Chain F: Y.190, M.193, W.197, F.316, N.321, I.323, N.479, T.481 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.321, F:N.479 GOL.51: 7 residues within 4Å: Chain G: Y.190, M.193, W.197, N.321, I.323, N.479, T.481 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:Y.190, G:N.321, G:N.479 Water bridges: G:N.479, G:T.481 GOL.58: 8 residues within 4Å: Chain H: Y.190, M.193, W.197, F.316, N.321, I.323, N.479, T.481 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Y.190, H:N.321, H:N.321 Water bridges: H:N.479, H: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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Formyltetrahydrofolate dehydrogenase

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