SMTL ID : 3rhr.1

Crystal structure of the C707A mutant of the C-Terminal domain of 10'FORMYLTETRAHYDROFOLATE DEHYDROGENASE in complex with NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NDP.1: 29 residues within 4Å: Chain A: V.185, I.186, P.187, W.188, N.189, M.194, 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, E.288, L.289, G.290, G.291, A.322, E.419, F.421, L.449, F.487 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.187, A:T.264, A:A.322 Hydrogen bonds: A:I.186, A:K.212, A:Q.215, A:G.245, A:Q.250, A:S.266, A:L.289, A:G.291, A:E.419 Water bridges: A:Q.250, A:S.253, A:S.266, A:T.267 Salt bridges: A:K.212 NDP.11: 29 residues within 4Å: Chain B: V.185, I.186, P.187, W.188, N.189, M.194, 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, E.288, L.289, G.290, G.291, A.322, E.419, F.421, L.449, F.487 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:P.187, B:T.264, B:A.322 Hydrogen bonds: B:I.186, B:K.212, B:Q.215, B:G.245, B:Q.250, B:S.266, B:E.288, B:L.289, B:G.291, B:E.419 Water bridges: B:S.246, B:S.253, B:G.290 Salt bridges: B:K.212 NDP.19: 30 residues within 4Å: Chain C: V.185, I.186, P.187, W.188, N.189, M.194, 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, E.288, L.289, G.290, G.291, A.322, E.419, F.421, L.449, F.487 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.187, C:T.264, C:A.322 Hydrogen bonds: C:I.186, C:K.212, C:Q.215, C:G.245, C:Q.250, C:S.266, C:E.288, C:L.289, C:G.291, C:E.419 Water bridges: C:Q.215, C:Q.215, C:V.216, C:S.246, C:Q.250, C:S.253, C:T.267, C:E.419, C:E.419 Salt bridges: C:K.212 NDP.28: 30 residues within 4Å: Chain D: V.185, I.186, P.187, W.188, N.189, M.194, 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, E.288, L.289, G.290, G.291, A.322, E.419, F.421, L.449, F.487 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:P.187, D:T.264, D:A.322 Hydrogen bonds: D:I.186, D:K.212, D:Q.215, D:G.245, D:Q.250, D:S.266, D:L.289, D:G.291, D:E.419 Water bridges: D:W.188, D:Q.215, D:Q.215, D:V.216, D:S.246, D:S.253, D:G.290, D:E.419, D:E.419 Salt bridges: D:K.212

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

SO4.2: 3 residues within 4Å: Chain A: D.466, K.467 Chain C: R.169 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: R.251, P.256 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: R.379, Y.414 Ligand excluded by PLIP SO4.5: 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 SO4.6: 4 residues within 4Å: Chain A: R.166, R.169 Chain C: Y.463, K.467 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: N.163 Chain B: Q.143 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: Q.143 Chain B: N.163 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: T.60, N.353, E.356, R.396 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: D.466, K.467 Chain D: R.169 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain B: R.251, P.256 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: R.379, Y.414 Ligand excluded by PLIP SO4.15: 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 SO4.16: 3 residues within 4Å: Chain B: R.166, R.169 Chain D: Y.463 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: T.60, N.353, E.356, R.396 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: R.169 Chain C: D.466, K.467 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain C: R.251, P.256 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: R.379, Y.414 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain C: K.284, L.508, R.509, I.510 Chain D: F.495, G.496, K.497 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: Y.463, K.467 Chain C: R.166, R.169 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: T.60, N.353, R.396 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain C: K.30, R.357 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: R.169 Chain D: D.466, K.467 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain D: R.251, P.256 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain D: R.379, Y.414 Ligand excluded by PLIP SO4.32: 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 SO4.33: 3 residues within 4Å: Chain B: Y.463 Chain D: R.166, R.169 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain C: N.163 Chain D: K.135, Q.143 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain D: T.60, N.353, E.356, R.396 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: Y.190, M.193, N.321, I.323, N.479, T.481 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.190, A:N.321, A:T.481, A:T.481 Water bridges: A:T.481 GOL.18: 7 residues within 4Å: Chain B: T.136, Y.190, M.193, N.321, I.323, N.479, T.481 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.321, B:T.481, B:T.481 Water bridges: B:T.481 GOL.27: 7 residues within 4Å: Chain C: T.136, Y.190, M.193, W.197, N.321, N.479, T.481 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.321, C:T.481 GOL.36: 7 residues within 4Å: Chain D: T.136, Y.190, M.193, W.197, N.321, I.323, 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., Conserved catalytic residues of the ALDH1L1 aldehyde dehydrogenase domain control binding and discharging of the coenzyme. J.Biol.Chem. (2011)

Release Date

2011-04-27

Peptides

Aldehyde dehydrogenase 1 family, member L1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aldehyde dehydrogenase 1 family, member L1

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