SMTL ID : 4i8q.1

Structure of the aminoaldehyde dehydrogenase 1 E260A mutant from Solanum lycopersicum (SlAMADH1-E260A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: I.171, T.172, P.173, W.174, N.175, M.180, K.198, P.199, S.200, E.201, G.231, P.232, G.235, G.236, F.249, T.250, G.251, S.252, T.255, I.259, A.273, L.274, G.275, C.308, E.407, F.409, L.435, W.473 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.173, A:T.250 Hydrogen bonds: A:T.172, A:T.172, A:W.174, A:K.198, A:S.200, A:E.201, A:S.252, A:T.255, A:L.274, A:E.407, A:E.407 NAD.13: 28 residues within 4Å: Chain B: I.171, T.172, P.173, W.174, N.175, M.180, K.198, P.199, S.200, E.201, G.231, P.232, G.235, G.236, F.249, T.250, G.251, S.252, T.255, I.259, A.273, L.274, G.275, C.308, E.407, F.409, L.435, W.473 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.173, B:T.250 Hydrogen bonds: B:T.172, B:T.172, B:W.174, B:K.198, B:S.200, B:E.201, B:S.252, B:T.255, B:L.274, B:E.407, B:E.407

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

EDO.2: 3 residues within 4Å: Chain A: T.48, E.50, K.385 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.48, A:E.50, A:K.385 EDO.3: 2 residues within 4Å: Chain A: I.337, H.382 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.337 Water bridges: A:Q.381 EDO.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: I.51, I.52, G.53 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.52 EDO.6: 1 residues within 4Å: Chain B: T.503 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.503 EDO.8: 1 residues within 4Å: Chain A: E.357 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.357 EDO.9: 5 residues within 4Å: Chain A: D.126, W.183, T.467, F.468, N.469 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.126, A:D.126, A:W.183, A:N.469 EDO.14: 3 residues within 4Å: Chain B: T.48, E.50, K.385 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.48, B:E.50, B:K.385 EDO.15: 2 residues within 4Å: Chain B: I.337, H.382 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.337 Water bridges: B:Q.381 EDO.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain B: I.51, I.52, G.53 1 PLIP interactions: 1 interactions with chain B Water bridges: B:I.52 EDO.18: 1 residues within 4Å: Chain A: T.503 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.503 EDO.20: 1 residues within 4Å: Chain B: E.357 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.357 EDO.21: 5 residues within 4Å: Chain B: D.126, W.183, T.467, F.468, N.469 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.126, B:D.126, B:W.183, B:N.469

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

PEG.7: 2 residues within 4Å: Chain A: A.505, E.506 No protein-ligand interaction detected (PLIP) PEG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.19: 2 residues within 4Å: Chain B: A.505, E.506 No protein-ligand interaction detected (PLIP) PEG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.12: 3 residues within 4Å: Chain A: I.44, D.112, L.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.44, A:D.112, A:D.112 NA.24: 3 residues within 4Å: Chain B: I.44, D.112, L.202 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.44, B:I.44, B:D.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopecny, D. et al., Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate. J.Biol.Chem. (2013)

Release Date

2013-02-20

Peptides

Putative betaine aldehyde dehyrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative betaine aldehyde dehyrogenase