SMTL ID : 7qk9.1

Crystal structure of the ALDH1A3-ATP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-tetramer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: I.158, T.159, P.160, W.161, K.185, A.187, E.188, G.218, G.222, A.223, F.236, T.237, G.238, S.239, V.242, L.245, V.246 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.159, A:W.161, A:W.161, A:K.185, A:E.188, A:S.239, A:S.239 Water bridges: A:N.162, A:Q.189, A:Q.189, A:Q.189, A:Q.189, A:G.218, A:S.239, A:S.239, A:L.245 ATP.8: 17 residues within 4Å: Chain B: I.158, T.159, W.161, K.185, P.186, A.187, E.188, G.218, G.222, A.223, F.236, T.237, G.238, S.239, V.242, V.246, Q.342 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.159, B:T.159, B:K.185, B:E.188, B:Q.189, B:S.239, B:Q.342 Water bridges: B:G.218, B:S.239, B:S.239 ATP.13: 17 residues within 4Å: Chain C: I.158, T.159, P.160, W.161, K.185, A.187, E.188, G.218, G.222, A.223, F.236, T.237, G.238, S.239, V.242, L.245, V.246 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.159, C:W.161, C:W.161, C:K.185, C:E.188, C:S.239, C:S.239 Water bridges: C:N.162, C:Q.189, C:Q.189, C:Q.189, C:Q.189, C:G.218, C:S.239, C:S.239, C:L.245 ATP.20: 17 residues within 4Å: Chain D: I.158, T.159, W.161, K.185, P.186, A.187, E.188, G.218, G.222, A.223, F.236, T.237, G.238, S.239, V.242, V.246, Q.342 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:T.159, D:T.159, D:K.185, D:E.188, D:Q.189, D:S.239, D:Q.342 Water bridges: D:G.218, D:S.239, D:S.239

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

PEG.2: 9 residues within 4Å: Chain A: G.117, R.120, T.121, L.166, W.170, L.452, Y.453, A.454 Ligands: P4C.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.121, A:W.170 PEG.5: 8 residues within 4Å: Chain A: I.132, G.134, R.148, H.149 Chain C: T.136, I.137, P.138, C.145 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:I.137, C:C.145, A:H.149, A:H.149 Water bridges: C:C.145 PEG.9: 8 residues within 4Å: Chain B: G.117, R.120, T.121, L.166, W.170, L.452, A.454, L.470 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.121, B:W.170 PEG.10: 5 residues within 4Å: Chain A: K.135, A.476 Chain B: Y.473, A.476 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.135 PEG.14: 9 residues within 4Å: Chain C: G.117, R.120, T.121, L.166, W.170, L.452, Y.453, A.454 Ligands: P4C.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.170 PEG.17: 8 residues within 4Å: Chain A: T.136, I.137, P.138, C.145 Chain C: I.132, G.134, R.148, H.149 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:I.137, A:C.145, C:H.149, C:H.149 Water bridges: A:C.145 PEG.21: 8 residues within 4Å: Chain D: G.117, R.120, T.121, L.166, W.170, L.452, A.454, L.470 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.170 PEG.22: 5 residues within 4Å: Chain C: K.135, A.476 Chain D: Y.473, A.476 Ligands: GOL.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.135

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.247, R.257, V.258 Chain B: K.247, V.258, N.466 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:K.247, B:V.258, A:K.247, A:V.258, A:V.258 Water bridges: A:T.259, A:T.259 GOL.4: 3 residues within 4Å: Chain A: K.320, C.362, G.363 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.363 Water bridges: A:E.361 GOL.7: 6 residues within 4Å: Chain A: E.472, Y.473, A.476 Chain B: K.135, H.149 Ligands: PEG.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.135, B:K.135 GOL.15: 6 residues within 4Å: Chain C: K.247, R.257, V.258 Chain D: K.247, V.258, N.466 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:K.247, D:V.258, C:K.247, C:V.258, C:V.258 Water bridges: C:T.259, C:E.477 GOL.16: 3 residues within 4Å: Chain C: K.320, C.362, G.363 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.363 Water bridges: C:E.361 GOL.19: 6 residues within 4Å: Chain C: E.472, Y.473, A.476 Chain D: K.135, H.149 Ligands: PEG.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.135, D:K.135

4 x P4C: O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL(Covalent)

P4C.6: 12 residues within 4Å: Chain A: I.113, N.162, F.163, L.166, M.167, W.170, F.289, C.294, C.295, N.450, L.452 Ligands: PEG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.162, A:C.295, A:L.452 P4C.12: 12 residues within 4Å: Chain B: I.113, N.162, F.163, L.166, M.167, W.170, F.289, C.294, C.295, T.296, N.450, L.452 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.162, B:C.295 Water bridges: B:N.450 P4C.18: 12 residues within 4Å: Chain C: I.113, N.162, F.163, L.166, M.167, W.170, F.289, C.294, C.295, N.450, L.452 Ligands: PEG.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.162, C:C.295, C:L.452 P4C.24: 12 residues within 4Å: Chain D: I.113, N.162, F.163, L.166, M.167, W.170, F.289, C.294, C.295, T.296, N.450, L.452 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.162, D:C.295 Water bridges: D:N.450

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 4 residues within 4Å: Chain B: R.70, R.148, E.150, P.151 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.70, B:R.148 SO4.23: 4 residues within 4Å: Chain D: R.70, R.148, E.150, P.151 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.70, D:R.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Castellvi, A. et al., Structural and biochemical evidence that ATP inhibits the cancer biomarker human aldehyde dehydrogenase 1A3. Commun Biol (2022)

Release Date

2022-04-20

Peptides

Aldehyde dehydrogenase family 1 member A3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Aldehyde dehydrogenase family 1 member A3

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