SMTL ID : 4pz2.1

Structure of Zm ALDH2-6 (RF2F) in complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: T.70, R.71, D.139, Q.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.71, A:D.139 NA.7: 4 residues within 4Å: Chain B: T.70, R.71, D.139, Q.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.71, B:D.139 NA.9: 4 residues within 4Å: Chain C: T.70, R.71, D.139, Q.226 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.70, C:R.71, C:D.139, C:D.139 NA.15: 4 residues within 4Å: Chain D: T.70, R.71, D.139, Q.226 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.70, D:T.70, D:R.71

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

PEG.2: 4 residues within 4Å: Chain A: S.64, G.65, R.66, T.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.64, A:T.67, A:T.67 Water bridges: A:T.67

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

NAD.3: 29 residues within 4Å: Chain A: I.195, I.196, P.197, W.198, N.199, M.204, K.222, P.223, A.224, E.225, G.255, P.256, G.259, A.260, F.273, T.274, G.275, S.276, V.279, L.282, I.283, E.298, L.299, G.300, C.332, E.432, F.434, L.460, F.498 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.197, A:T.274 Hydrogen bonds: A:I.196, A:W.198, A:K.222, A:E.225, A:S.276, A:E.298, A:E.432 Water bridges: A:Q.226, A:Q.226, A:Q.380 NAD.8: 29 residues within 4Å: Chain B: I.195, I.196, P.197, W.198, N.199, M.204, K.222, P.223, A.224, E.225, G.255, P.256, G.259, A.260, F.273, T.274, G.275, S.276, V.279, L.282, I.283, E.298, L.299, G.300, C.332, E.432, F.434, L.460, F.498 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.197, B:T.274 Hydrogen bonds: B:I.196, B:I.196, B:W.198, B:K.222, B:E.225, B:S.276, B:E.298, B:E.298, B:E.432 Water bridges: B:P.256, B:Q.380 NAD.14: 31 residues within 4Å: Chain C: I.195, I.196, P.197, W.198, N.199, M.204, K.222, P.223, A.224, E.225, G.255, P.256, G.259, A.260, F.273, T.274, G.275, S.276, V.279, L.282, I.283, E.298, L.299, G.300, C.332, E.432, F.434, L.460, F.498 Ligands: EDO.10, EDO.13 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:P.197, C:T.274 Hydrogen bonds: C:I.196, C:W.198, C:K.222, C:E.225, C:S.276, C:E.298, C:E.298, C:E.432 NAD.17: 29 residues within 4Å: Chain D: I.195, I.196, P.197, W.198, N.199, M.204, K.222, P.223, A.224, E.225, G.255, P.256, G.259, A.260, F.273, T.274, G.275, S.276, V.279, L.282, I.283, E.298, L.299, G.300, C.332, E.432, F.434, L.460, F.498 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:P.197, D:T.274 Hydrogen bonds: D:I.196, D:W.198, D:K.222, D:E.225, D:S.276, D:E.298, D:E.298, D:E.432

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

EDO.4: 3 residues within 4Å: Chain A: V.207, M.492, F.498 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain A: F.308, Q.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.341, A:Q.341 EDO.6: 5 residues within 4Å: Chain A: Q.181, H.183 Chain C: N.473 Chain D: Q.181, H.183 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.183, A:Q.181 EDO.10: 3 residues within 4Å: Chain C: M.204, F.498 Ligands: NAD.14 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.154 EDO.11: 3 residues within 4Å: Chain C: F.308, D.309, Q.341 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.309, C:Q.341 EDO.12: 3 residues within 4Å: Chain C: N.454, D.455, T.456 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.454 EDO.13: 4 residues within 4Å: Chain C: Q.380, R.383, E.432 Ligands: NAD.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.383, C:E.432 EDO.16: 4 residues within 4Å: Chain C: R.160, G.164 Chain D: G.115, A.119 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

ZmALDH: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ZmALDH