SMTL ID : 4gnz.1

Crystal structure of the c707s mutant of c-terminal domain of 10'formyltetrahydrofolate dehydrogenase in complex with NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.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, 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, S.322, E.419, F.421, L.449, F.487 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.187, A:T.264 Hydrogen bonds: A:I.186, A:K.212, A:Q.215, A:Q.215, A:G.245, A:Q.250, A:S.266, A:H.272, A:L.289, A:G.291, A:S.322, A:E.419 Water bridges: A:W.188, A:W.188, A:S.246, A:Q.250, A:T.267 Salt bridges: A:K.212 NAP.13: 28 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, S.322, E.419, F.421, L.449, F.487 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:P.187, B:T.264 Hydrogen bonds: B:I.186, B:K.212, B:Q.215, B:G.245, B:Q.250, B:S.266, B:H.272, B:E.288, B:L.289, B:G.291, B:S.322, B:E.419 Water bridges: B:W.188, B:Q.215, B:Q.215, B:S.246, B:S.276, B:G.290 Salt bridges: B:K.212 NAP.21: 29 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, S.322, E.419, F.421, L.449, F.487 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:P.187, C:T.264 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:S.322, C:E.419 Water bridges: C:V.216, C:S.246, C:S.246, C:Q.250, C:T.267, C:E.419, C:E.419, C:E.419 Salt bridges: C:K.212 NAP.29: 29 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, S.322, E.419, F.421, L.449, F.487 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.187, D:T.264 Hydrogen bonds: D:I.186, D:K.212, D:Q.215, D:G.245, D:Q.250, D:S.266, D:L.289, D:S.322, D:E.419 Water bridges: D:W.188, D:W.188, D:Q.215, D:Q.215, D:V.216, D:S.246, D:S.246, D:S.276 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: 3 residues within 4Å: Chain A: R.169 Chain C: D.466, K.467 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: R.251, P.256 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.379, Y.414 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: R.166, R.169 Chain C: Y.463 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: N.163 Chain B: Q.143 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: K.135, 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 SO4.10: 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 SO4.11: 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 SO4.14: 3 residues within 4Å: Chain B: R.169 Chain D: D.466, K.467 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: D.466, K.467 Chain D: R.169 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: R.251, P.256 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: R.379, Y.414 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: R.166, R.169 Chain D: Y.463, K.467 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: T.60, N.353, E.356, R.396 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: R.251, P.256 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain C: R.379, Y.414 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: 4 residues within 4Å: Chain C: T.60, N.353, E.356, R.396 Ligand excluded by PLIP SO4.26: 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 SO4.27: 2 residues within 4Å: Chain C: K.30, R.357 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: 3 residues within 4Å: Chain B: Y.463 Chain D: R.166, R.169 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain C: N.163 Chain D: K.135, Q.143 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain D: T.60, N.353, R.396 Ligand excluded by PLIP SO4.35: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 7 residues within 4Å: Chain A: Y.190, M.193, W.197, F.316, N.321, N.479, T.481 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.321 GOL.20: 6 residues within 4Å: Chain B: Y.190, W.197, F.316, N.321, N.479, T.481 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.321 GOL.28: 7 residues within 4Å: Chain C: Y.190, M.193, W.197, F.316, N.321, N.479, T.481 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.321 GOL.36: 7 residues within 4Å: Chain D: Y.190, M.193, W.197, F.316, N.321, N.479, T.481 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.321 Water bridges: D:S.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsybovsky, Y. et al., The mechanism of discrimination between oxidized and reduced coenzyme in the aldehyde dehydrogenase domain of Aldh1l1. Chem.Biol.Interact (2013)

Release Date

2013-01-23

Peptides

Cytosolic 10-formyltetrahydrofolate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cytosolic 10-formyltetrahydrofolate dehydrogenase

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