SMTL ID : 5mz5.1

Crystal structure of aldehyde dehydrogenase 21 (ALDH21) from Physcomitrella patens in its apoform

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.139, F.190, N.193, L.194, Y.314, I.321, R.475, Y.481 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.139, A:R.139, A:N.193, A:Y.481 GOL.2: 5 residues within 4Å: Chain A: D.296, Y.297, R.331, L.332, K.449 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.296, A:Y.297, A:Y.297, A:R.331 Water bridges: A:K.449 GOL.3: 8 residues within 4Å: Chain A: E.150, R.153, I.154, K.176, K.495, M.498, D.499, L.502 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.150, A:R.153, A:D.499 GOL.8: 5 residues within 4Å: Chain B: D.296, Y.297, R.331, L.332, K.449 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.296, B:Y.297, B:Y.297, B:R.331 Water bridges: B:R.331, B:K.449 GOL.9: 8 residues within 4Å: Chain B: R.139, F.190, N.193, L.194, Y.314, I.321, R.475, Y.481 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.139, B:R.139, B:N.193, B:R.475, B:Y.481 GOL.10: 7 residues within 4Å: Chain B: E.150, R.153, I.154, K.495, M.498, D.499, L.502 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.153, B:K.495 Water bridges: B:R.153, B:Y.155 GOL.16: 6 residues within 4Å: Chain C: E.150, R.153, I.154, K.495, M.498, D.499 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.150, C:K.495 Water bridges: C:R.153, C:Y.155 GOL.17: 5 residues within 4Å: Chain C: D.296, Y.297, R.331, L.332, K.449 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.296, C:Y.297, C:Y.297, C:R.331 Water bridges: C:K.449, C:K.449 GOL.18: 9 residues within 4Å: Chain C: R.139, F.190, N.193, L.194, Y.314, S.319, I.321, R.475, Y.481 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.139, C:R.139, C:N.193, C:Y.314, C:R.475, C:Y.481 GOL.22: 8 residues within 4Å: Chain C: K.274, K.281, V.282, I.489 Chain D: K.274, K.281, V.282, I.489 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:V.282, C:V.282 GOL.23: 8 residues within 4Å: Chain D: R.139, F.190, N.193, L.194, Y.314, I.321, R.475, Y.481 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.139, D:R.139, D:N.193, D:Y.314, D:Y.314, D:Y.481 GOL.24: 7 residues within 4Å: Chain D: E.150, R.153, I.154, K.176, K.495, M.498, D.499 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.150, D:E.150, D:K.176, D:K.495 Water bridges: D:R.153, D:Y.155

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

EDO.4: 5 residues within 4Å: Chain A: G.267, P.268, W.271, D.486 Chain B: K.279 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.268 EDO.5: 5 residues within 4Å: Chain A: K.281, V.282 Chain B: K.281, V.282, I.489 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.282, B:V.282, A:V.282, A:V.282 EDO.7: 6 residues within 4Å: Chain A: N.511, T.514, L.515 Chain B: V.298, P.299 Chain C: N.452 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.511, A:L.515 Water bridges: A:N.511 EDO.11: 3 residues within 4Å: Chain B: V.341, A.342, K.345 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.342 EDO.12: 4 residues within 4Å: Chain B: Y.40, N.41, F.43, E.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.41, B:N.41 EDO.13: 6 residues within 4Å: Chain B: W.188, Q.318, M.362, A.367, I.371, F.416 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.416 EDO.14: 3 residues within 4Å: Chain B: D.450, N.452 Chain C: K.449 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.452 EDO.19: 5 residues within 4Å: Chain A: L.515 Chain B: K.449 Chain C: D.450, N.452, K.453 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.452 EDO.20: 4 residues within 4Å: Chain C: Y.155, G.156, E.157, K.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.176, C:K.176 EDO.21: 1 residues within 4Å: Chain C: F.416 No protein-ligand interaction detected (PLIP) EDO.25: 4 residues within 4Å: Chain D: D.296, Y.297, R.331, K.449 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.297, D:Y.297 Water bridges: D:K.449

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

PEG.6: 4 residues within 4Å: Chain A: K.449, D.450 Chain D: K.449, D.450 No protein-ligand interaction detected (PLIP) PEG.15: 4 residues within 4Å: Chain B: K.449, D.450 Chain C: K.449, D.450 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.450, B:D.450 Water bridges: C:K.449, C:D.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopecna, M. et al., The ALDH21 gene found in lower plants and some vascular plants codes for a NADP(+) -dependent succinic semialdehyde dehydrogenase. Plant J. (2017)

Release Date

2017-08-09

Peptides

ALDH21): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ALDH21)

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