SMTL ID : 6qap.1

Structure of the human aldehyde dehydrogenase 9A1 in C2 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: S.243, Y.490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.243 EDO.2: 2 residues within 4Å: Chain A: K.241, V.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.242, A:V.242 Water bridges: A:C.234 EDO.3: 9 residues within 4Å: Chain A: P.25, L.26, N.27, V.34, E.35, P.36, F.57, T.58, Q.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.26, A:N.27, A:E.35, A:T.58 EDO.4: 6 residues within 4Å: Chain A: Q.129, E.132, Y.133 Chain D: C.88, G.136, A.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.129, A:E.132 EDO.5: 8 residues within 4Å: Chain A: G.168, A.169, P.173, F.193, P.195, S.196, T.199, A.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.173, A:S.196, A:S.196 Water bridges: A:A.203 EDO.6: 5 residues within 4Å: Chain B: E.132, Y.133, G.136 Chain C: G.136 Ligands: PEG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.136 EDO.7: 3 residues within 4Å: Chain B: R.481, R.485 Chain C: R.481 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.485, C:R.481 Water bridges: C:R.485, C:R.485 EDO.8: 3 residues within 4Å: Chain B: S.243, T.487, Y.490 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain C: S.23, Q.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.23 EDO.22: 5 residues within 4Å: Chain A: G.136 Chain D: E.132, Y.133, G.136 Ligands: NA.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.136 EDO.23: 9 residues within 4Å: Chain D: G.31, S.211, V.215, P.216, P.217, G.218, L.219, F.220 Ligands: NA.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.218, D:F.220 EDO.24: 7 residues within 4Å: Chain D: L.26, N.27, E.35, P.36, F.57, T.58, Q.224 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.35, D:T.58, D:T.58 EDO.25: 4 residues within 4Å: Chain D: S.211, E.212, A.213, G.214 3 PLIP interactions: 3 interactions with chain D Water bridges: D:E.93, D:E.212, D:A.213 EDO.26: 4 residues within 4Å: Chain D: I.117, F.118, R.121, L.122 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.121 EDO.27: 5 residues within 4Å: Chain C: E.482 Chain D: A.142, G.143, R.157, R.158 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.158, C:E.482

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

PEG.9: 3 residues within 4Å: Chain B: D.38, A.39, K.63 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.38, B:A.39, B:K.63 PEG.14: 5 residues within 4Å: Chain C: S.243, F.244, V.486, T.487, Y.490 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.243 Water bridges: C:F.244 PEG.15: 10 residues within 4Å: Chain B: M.85, C.88, G.136, A.139 Chain C: L.92, Q.129, E.132, Y.133, G.136 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.132 PEG.16: 8 residues within 4Å: Chain C: I.167, G.168, K.194, P.195, S.196, P.197, G.226, A.227 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.168, C:G.168, C:K.194

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

NA.10: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain C Water bridges: C:W.170, C:N.171, C:N.171, C:N.171 NA.11: 2 residues within 4Å: Chain C: Q.24, E.208 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.24, C:Q.24 NA.12: 3 residues within 4Å: Chain C: V.22, S.23, Q.24 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.23, C:S.23, C:Q.24 NA.17: 8 residues within 4Å: Chain D: Y.28, R.29, G.30, G.31, G.218, F.220, N.221 Ligands: EDO.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.31, D:G.218, D:F.220 NA.18: 4 residues within 4Å: Chain A: C.88 Chain D: Q.129, E.132 Ligands: EDO.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.129 NA.19: 6 residues within 4Å: Chain D: G.168, A.169, P.173, P.195, S.196, T.199 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.169, D:S.196, D:T.199 NA.20: 3 residues within 4Å: Chain D: V.22, S.23, Q.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.23, D:Q.24, D:Q.24 NA.21: 2 residues within 4Å: Chain D: Q.24, E.208 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.24, D:E.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koncitikova, R. et al., Kinetic and structural analysis of human ALDH9A1. Biosci.Rep. (2019)

Release Date

2019-04-10

Peptides

4-trimethylaminobutyraldehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

4-trimethylaminobutyraldehyde dehydrogenase

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