SMTL ID : 6ljh.1

Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua in complex with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: C.48, H.49, T.50, C.177, T.181, G.202, I.203, G.204, T.205, V.206, D.226, V.227, N.228, K.231, C.273, T.274, G.275, V.276, L.279, I.297, G.298, A.299 Ligands: ZN.3, NA.8, NA.9 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:I.203, A:G.204, A:V.206, A:V.227, A:K.231, A:T.274, A:A.299 Water bridges: A:H.49, A:T.181, A:T.205, A:T.205, A:G.207 Salt bridges: A:K.231 NAD.12: 25 residues within 4Å: Chain B: C.48, H.49, T.50, C.177, T.181, G.202, I.203, G.204, T.205, V.206, D.226, V.227, N.228, K.231, C.273, T.274, G.275, V.276, L.279, I.297, G.298, A.299 Ligands: ZN.14, NA.19, NA.20 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.181, B:I.203, B:G.204, B:V.206, B:V.227, B:K.231, B:T.274, B:A.299 Water bridges: B:H.49, B:T.181, B:T.205, B:T.205, B:G.207 Salt bridges: B:K.231

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.99, G.100, C.102, C.105, C.113, H.114 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.99, A:C.102, A:C.105, A:C.113 ZN.3: 5 residues within 4Å: Chain A: C.48, H.69, E.70, C.177 Ligands: NAD.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.48, A:H.69, A:E.70, A:C.177 ZN.13: 6 residues within 4Å: Chain B: C.99, G.100, C.102, C.105, C.113, H.114 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.99, B:C.102, B:C.105, B:C.113 ZN.14: 5 residues within 4Å: Chain B: C.48, H.69, E.70, C.177 Ligands: NAD.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.48, B:H.69, B:E.70, B:C.177

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: S.20, G.21, P.22, V.23, V.52, T.55, K.56, Q.360, F.363 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.23, A:T.55, A:T.55, A:K.56, A:Q.360, A:Q.360 GOL.5: 9 residues within 4Å: Chain A: S.119, L.123, M.124, H.142, A.144, S.145, A.155, D.156, Y.159 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.125, A:D.156, A:D.156, A:D.156 Water bridges: A:S.119, A:S.119, A:Y.159 GOL.6: 5 residues within 4Å: Chain A: E.285, I.289, L.310, I.311, R.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.316, A:R.316 Water bridges: A:E.285, A:N.308 GOL.7: 8 residues within 4Å: Chain A: G.275, V.276, P.277, L.280, G.298, A.299, G.300 Chain B: L.312 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.300 Water bridges: A:E.272, A:G.301, B:S.309 GOL.15: 9 residues within 4Å: Chain B: S.20, G.21, P.22, V.23, V.52, T.55, K.56, Q.360, F.363 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.23, B:T.55, B:T.55, B:K.56, B:Q.360, B:Q.360 GOL.16: 9 residues within 4Å: Chain B: S.119, L.123, M.124, H.142, A.144, S.145, A.155, D.156, Y.159 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.125, B:D.156, B:D.156 Water bridges: B:S.119, B:S.119 GOL.17: 5 residues within 4Å: Chain B: E.285, I.289, L.310, I.311, R.316 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.316, B:R.316 Water bridges: B:N.308 GOL.18: 8 residues within 4Å: Chain A: L.312 Chain B: G.275, V.276, P.277, L.280, G.298, A.299, G.300 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:S.309, B:E.272, B:E.272, B:G.301 Hydrogen bonds: B:G.300

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

NA.8: 3 residues within 4Å: Chain A: C.48, H.49 Ligands: NAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.49 Water bridges: A:L.47 NA.9: 4 residues within 4Å: Chain A: I.297, G.298, A.299 Ligands: NAD.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.297 NA.10: 4 residues within 4Å: Chain A: K.41, M.42, L.43, E.380 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.42 NA.11: 4 residues within 4Å: Chain A: A.35, S.36, E.37, D.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.35 Water bridges: A:E.37, A:N.158 NA.19: 3 residues within 4Å: Chain B: C.48, H.49 Ligands: NAD.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.49 Water bridges: B:L.47 NA.20: 4 residues within 4Å: Chain B: I.297, G.298, A.299 Ligands: NAD.12 No protein-ligand interaction detected (PLIP) NA.21: 4 residues within 4Å: Chain B: K.41, M.42, L.43, E.380 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.380 NA.22: 4 residues within 4Å: Chain B: A.35, S.36, E.37, D.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.36 Water bridges: B:N.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z., Crystal structure of Alcohol dehydrogenase 1 from Artemisia annua in complex with NAD+. To Be Published

Release Date

2020-12-23

Peptides

Alcohol dehydrogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alcohol dehydrogenase 1

Related Entries With Identical Sequence