SMTL ID : 7qk8.1

Crystal structure of the ALDH1A3-NAD+ complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: I.194, T.195, P.196, W.197, N.198, M.203, K.221, A.223, E.224, G.254, G.258, A.259, F.272, T.273, G.274, S.275, V.278, L.281, V.282, E.297, L.298, G.299, C.331, E.428, F.430, L.456, F.494 Ligands: P4C.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.196, A:T.273 Hydrogen bonds: A:T.195, A:T.195, A:W.197, A:K.221, A:E.224, A:S.275, A:E.297, A:E.297, A:E.428 Water bridges: A:N.198, A:Q.225, A:Q.225, A:G.254, A:T.276, A:L.281 NAD.9: 27 residues within 4Å: Chain B: I.194, T.195, P.196, W.197, N.198, M.203, K.221, P.222, A.223, E.224, G.254, G.258, A.259, F.272, T.273, G.274, S.275, V.278, V.282, E.297, L.298, G.299, C.331, F.430, L.456, F.494 Ligands: P4C.13 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.196, B:T.273 Hydrogen bonds: B:T.195, B:T.195, B:W.197, B:K.221, B:E.224, B:S.275, B:S.275, B:E.297, B:E.297 Water bridges: B:N.198, B:Q.225, B:G.254, B:L.281, B:G.300 NAD.17: 28 residues within 4Å: Chain C: I.194, T.195, P.196, W.197, N.198, M.203, K.221, A.223, E.224, G.254, G.258, A.259, F.272, T.273, G.274, S.275, V.278, L.281, V.282, E.297, L.298, G.299, C.331, E.428, F.430, L.456, F.494 Ligands: P4C.21 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:P.196, C:T.273 Hydrogen bonds: C:T.195, C:T.195, C:W.197, C:K.221, C:E.224, C:S.275, C:E.297, C:E.428 Water bridges: C:N.198, C:Q.225, C:Q.225, C:G.254, C:T.276, C:L.281 NAD.25: 27 residues within 4Å: Chain D: I.194, T.195, P.196, W.197, N.198, M.203, K.221, P.222, A.223, E.224, G.254, G.258, A.259, F.272, T.273, G.274, S.275, V.278, V.282, E.297, L.298, G.299, C.331, F.430, L.456, F.494 Ligands: P4C.29 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:P.196, D:T.273 Hydrogen bonds: D:T.195, D:T.195, D:W.197, D:K.221, D:E.224, D:S.275, D:S.275, D:E.297 Water bridges: D:N.198, D:Q.225, D:G.254, D:L.281, D:G.300

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

PEG.2: 9 residues within 4Å: Chain A: G.153, R.156, T.157, L.202, W.206, L.488, Y.489, A.490, L.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.206 PEG.10: 7 residues within 4Å: Chain B: G.153, R.156, T.157, L.202, W.206, L.488, A.490 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.206 PEG.18: 9 residues within 4Å: Chain C: G.153, R.156, T.157, L.202, W.206, L.488, Y.489, A.490, L.506 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.157, C:W.206 PEG.26: 7 residues within 4Å: Chain D: G.153, R.156, T.157, L.202, W.206, L.488, A.490 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.157, D:W.206

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.283, R.293, V.294 Chain B: K.283, V.294, N.502 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: K.356, C.398, G.399 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: L.111, H.118, D.166, K.167 Chain D: H.118, R.159, Y.160 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: I.168, G.170, R.184, H.185 Chain C: T.172, I.173, P.174 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: E.508, Y.509 Chain B: K.171, H.185 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain B: A.310, D.311, L.312, D.313, R.350 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain B: K.47, F.48, T.49, K.50, W.57 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain B: T.172, I.173, P.174 Chain D: I.168, Q.169, G.170, R.184, H.185 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain B: Q.76, C.78, E.79 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain C: K.283, R.293, V.294 Chain D: K.283, V.294, N.502 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain C: K.356, C.398, G.399 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain B: H.118, R.159, Y.160 Chain C: L.111, H.118, D.166, K.167 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain A: T.172, I.173, P.174 Chain C: I.168, G.170, R.184, H.185 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain C: E.508, Y.509 Chain D: K.171, H.185 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain D: A.310, D.311, L.312, D.313, R.350 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain D: K.47, F.48, T.49, K.50, W.57 Ligand excluded by PLIP GOL.31: 8 residues within 4Å: Chain B: I.168, Q.169, G.170, R.184, H.185 Chain D: T.172, I.173, P.174 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain D: Q.76, C.78, E.79 Ligand excluded by PLIP

4 x P4C: O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL(Non-covalent)

P4C.5: 13 residues within 4Å: Chain A: I.149, F.199, M.203, W.206, Q.321, F.325, C.330, C.331, Y.485, N.486, L.488, F.494 Ligands: NAD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.486 P4C.13: 8 residues within 4Å: Chain B: I.149, F.199, F.325, C.330, C.331, N.486, L.488 Ligands: NAD.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.486 P4C.21: 13 residues within 4Å: Chain C: I.149, F.199, M.203, W.206, Q.321, F.325, C.330, C.331, Y.485, N.486, L.488, F.494 Ligands: NAD.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.486 P4C.29: 8 residues within 4Å: Chain D: I.149, F.199, F.325, C.330, C.331, N.486, L.488 Ligands: NAD.25 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.486

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

SO4.14: 4 residues within 4Å: Chain B: R.106, R.184, E.186, P.187 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.106, B:R.184, B:R.184 Salt bridges: B:R.106, B:R.184 SO4.30: 4 residues within 4Å: Chain D: R.106, R.184, E.186, P.187 5 PLIP interactions: 5 interactions with chain D Water bridges: D:R.106, D:R.184, D:R.184 Salt bridges: D:R.106, D:R.184

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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