SMTL ID : 4pxl.1

Structure of Zm ALDH2-3 (RF2C) in complex with NAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 29 residues within 4Å: Chain A: I.181, V.182, P.183, W.184, N.185, K.208, P.209, A.210, E.211, Q.212, G.241, P.242, G.245, A.246, F.259, T.260, G.261, S.262, V.265, L.268, E.284, L.285, G.286, C.318, Q.365, K.368, E.415, F.417 Ligands: CA.11 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.183, A:F.417, A:F.417 Hydrogen bonds: A:V.182, A:K.208, A:E.211, A:Q.212, A:G.261, A:S.262, A:S.262, A:E.284, A:Q.365, A:Q.365, A:K.368 NAD.13: 28 residues within 4Å: Chain B: I.181, V.182, P.183, W.184, N.185, K.208, P.209, A.210, E.211, Q.212, G.241, P.242, G.245, A.246, F.259, T.260, G.261, S.262, V.265, L.268, E.284, L.285, G.286, C.318, Q.365, K.368, E.415, F.417 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.183, B:F.417, B:F.417 Hydrogen bonds: B:V.182, B:K.208, B:E.211, B:Q.212, B:G.261, B:S.262, B:S.262, B:E.284, B:Q.365, B:Q.365, B:K.368, B:E.415 Water bridges: B:Q.212 NAD.19: 29 residues within 4Å: Chain C: I.181, V.182, P.183, W.184, N.185, K.208, P.209, A.210, E.211, Q.212, G.241, P.242, G.245, A.246, F.259, T.260, G.261, S.262, V.265, L.268, E.284, L.285, G.286, C.318, Q.365, K.368, E.415, F.417 Ligands: CA.29 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:P.183, C:F.417, C:F.417 Hydrogen bonds: C:V.182, C:K.208, C:E.211, C:Q.212, C:G.261, C:S.262, C:S.262, C:E.284, C:Q.365, C:Q.365, C:K.368 Water bridges: C:Q.212 NAD.31: 28 residues within 4Å: Chain D: I.181, V.182, P.183, W.184, N.185, K.208, P.209, A.210, E.211, Q.212, G.241, P.242, G.245, A.246, F.259, T.260, G.261, S.262, V.265, L.268, E.284, L.285, G.286, C.318, Q.365, K.368, E.415, F.417 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:P.183, D:F.417, D:F.417 Hydrogen bonds: D:V.182, D:K.208, D:E.211, D:Q.212, D:G.261, D:S.262, D:S.262, D:E.284, D:Q.365, D:Q.365, D:K.368, D:E.415 Water bridges: D:Q.212

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: V.347, G.348, C.390, G.391, Y.396 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: G.287, K.288, S.289, P.290, Y.441, G.442, L.443, A.444, A.464 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: T.159, L.160, K.161 Chain D: V.155, H.156, G.157, T.170, L.171, K.172 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: F.294, D.296, Q.327, V.454 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: T.263, E.264, R.267, R.440, M.486 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: D.453, N.456, T.457 Chain D: P.510, L.511, Y.512 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain B: Y.512 Chain D: D.453 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: R.94 Chain C: N.513, T.514, P.515 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: R.267 Chain B: M.252, E.275, S.276 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain C: V.347, G.348, C.390, G.391, Y.396 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain C: G.287, K.288, S.289, P.290, Y.441, G.442, L.443, A.444, A.464 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain B: V.155, H.156, G.157, T.170, L.171, K.172 Chain C: T.159, L.160, K.161 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain C: F.294, D.296, Q.327, V.454 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: T.263, E.264, R.267, R.440, M.486 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: P.510, L.511, Y.512 Chain D: D.453, N.456, T.457 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain B: D.453 Chain D: Y.512 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain A: N.513, T.514, P.515 Chain D: R.94 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: R.267 Chain D: M.252, E.275, S.276 Ligand excluded by PLIP

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 2 residues within 4Å: Chain A: E.340, K.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.340, A:K.344 PEG.5: 4 residues within 4Å: Chain A: N.451, D.453, V.454 Chain C: Y.512 No protein-ligand interaction detected (PLIP) PEG.7: 6 residues within 4Å: Chain D: F.294, D.296, Q.327, V.429, N.451, V.454 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.327 PEG.10: 4 residues within 4Å: Chain A: Y.186, T.189, F.473, F.475 No protein-ligand interaction detected (PLIP) PEG.21: 2 residues within 4Å: Chain C: E.340, K.344 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.340, C:K.344 PEG.23: 4 residues within 4Å: Chain A: Y.512 Chain C: N.451, D.453, V.454 No protein-ligand interaction detected (PLIP) PEG.25: 6 residues within 4Å: Chain B: F.294, D.296, Q.327, V.429, N.451, V.454 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.327 PEG.28: 4 residues within 4Å: Chain C: Y.186, T.189, F.473, F.475 No protein-ligand interaction detected (PLIP)

4 x NA: SODIUM ION(Non-functional Binders)

NA.9: 4 residues within 4Å: Chain A: T.56, R.57, D.125, Q.212 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.56, A:R.57, A:D.125 Water bridges: A:T.56 NA.16: 4 residues within 4Å: Chain B: T.56, R.57, D.125, Q.212 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.57, B:D.125 NA.27: 4 residues within 4Å: Chain C: T.56, R.57, D.125, Q.212 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.57, C:D.125, C:D.125 Water bridges: C:T.56 NA.34: 4 residues within 4Å: Chain D: T.56, R.57, D.125, Q.212 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.57, D:Q.212

2 x CA: CALCIUM ION(Non-functional Binders)

CA.11: 1 residues within 4Å: Ligands: NAD.1 No protein-ligand interaction detected (PLIP) CA.29: 1 residues within 4Å: Ligands: NAD.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koncitikova, R. et al., Role and structural characterization of plant aldehyde dehydrogenases from family 2 and family 7. Biochem.J. (2015)

Release Date

2015-03-18

Peptides

Cytosolic aldehyde dehydrogenase RF2C: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Cytosolic aldehyde dehydrogenase RF2C