SMTL ID : 1h2b.1

Crystal Structure of the Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum pernix at 1.65A Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

4 x OCA: OCTANOIC ACID (CAPRYLIC ACID)(Non-covalent)

OCA.1: 13 residues within 4Å: Chain A: C.54, T.56, W.65, H.79, F.128, L.131, D.168, L.308, V.309 Chain C: R.277, S.299 Ligands: NAJ.2, ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.128, A:L.131, A:L.308, A:V.309 Salt bridges: A:H.79 OCA.6: 11 residues within 4Å: Chain B: C.54, T.56, W.65, H.79, F.128, D.168, L.308, V.309 Chain D: S.299 Ligands: NAJ.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.308, B:V.309 Hydrogen bonds: B:T.56 Salt bridges: B:H.79 OCA.10: 13 residues within 4Å: Chain A: R.277, S.299 Chain C: C.54, T.56, W.65, H.79, F.128, L.131, D.168, L.308, V.309 Ligands: NAJ.11, ZN.12 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.128, C:L.131, C:L.308, C:V.309 Salt bridges: C:H.79 OCA.15: 11 residues within 4Å: Chain B: S.299 Chain D: C.54, T.56, W.65, H.79, F.128, D.168, L.308, V.309 Ligands: NAJ.16, ZN.17 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.308, D:V.309 Hydrogen bonds: D:T.56 Salt bridges: D:H.79

4 x NAJ: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)(Non-covalent)

NAJ.2: 32 residues within 4Å: Chain A: C.54, H.55, T.56, H.59, D.168, T.172, V.193, G.194, V.195, G.196, G.197, L.198, L.217, D.218, V.219, K.223, A.238, F.261, V.262, T.267, Y.270, V.284, G.285, Y.286, S.307, L.308, V.309, L.346, R.354 Chain C: I.298 Ligands: OCA.1, ZN.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.172 Hydrogen bonds: A:H.55, A:T.56, A:H.59, A:T.172, A:V.195, A:G.197, A:L.198, A:V.262, A:Y.270, A:V.284, A:Y.286, A:V.309 Water bridges: A:G.196, A:G.199, A:S.264, A:S.264, A:G.353, A:R.354, A:R.354 Salt bridges: A:H.55, A:R.354 NAJ.7: 32 residues within 4Å: Chain B: C.54, H.55, T.56, H.59, D.168, T.172, V.193, G.194, V.195, G.196, G.197, L.198, L.217, D.218, V.219, K.223, A.238, F.261, V.262, T.267, Y.270, V.284, G.285, Y.286, S.307, L.308, V.309, L.346, R.354 Chain D: I.298 Ligands: OCA.6, ZN.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:T.172, B:L.198 Hydrogen bonds: B:H.55, B:H.59, B:V.195, B:V.195, B:G.197, B:L.198, B:V.262, B:V.284, B:Y.286, B:V.309 Water bridges: B:G.196, B:G.199, B:S.264, B:S.264, B:G.353, B:R.354 Salt bridges: B:H.55, B:R.354 NAJ.11: 32 residues within 4Å: Chain A: I.298 Chain C: C.54, H.55, T.56, H.59, D.168, T.172, V.193, G.194, V.195, G.196, G.197, L.198, L.217, D.218, V.219, K.223, A.238, F.261, V.262, T.267, Y.270, V.284, G.285, Y.286, S.307, L.308, V.309, L.346, R.354 Ligands: OCA.10, ZN.12 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:T.172 Hydrogen bonds: C:H.55, C:T.56, C:H.59, C:T.172, C:V.195, C:G.197, C:L.198, C:V.262, C:Y.270, C:V.284, C:Y.286, C:V.309 Water bridges: C:G.196, C:G.199, C:S.264, C:S.264, C:G.353, C:R.354, C:R.354 Salt bridges: C:H.55, C:R.354 NAJ.16: 32 residues within 4Å: Chain B: I.298 Chain D: C.54, H.55, T.56, H.59, D.168, T.172, V.193, G.194, V.195, G.196, G.197, L.198, L.217, D.218, V.219, K.223, A.238, F.261, V.262, T.267, Y.270, V.284, G.285, Y.286, S.307, L.308, V.309, L.346, R.354 Ligands: OCA.15, ZN.17 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:T.172, D:L.198 Hydrogen bonds: D:H.55, D:H.59, D:V.195, D:V.195, D:G.197, D:L.198, D:V.262, D:V.284, D:Y.286, D:V.309 Water bridges: D:G.196, D:G.199, D:S.264, D:S.264, D:G.353, D:R.354 Salt bridges: D:H.55, D:R.354

10 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: C.54, T.56, H.79, D.168 Ligands: OCA.1, NAJ.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.54, A:H.79, A:D.168 ZN.4: 3 residues within 4Å: Chain A: D.332, H.334, R.345 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.332, A:D.332, A:H.334, H2O.12 ZN.5: 6 residues within 4Å: Chain A: D.109, G.110, C.112, C.115, C.123, E.124 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.109, A:C.112, A:C.115, A:C.123 ZN.8: 6 residues within 4Å: Chain B: C.54, T.56, H.79, D.168 Ligands: OCA.6, NAJ.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.54, B:H.79, B:D.168 ZN.9: 6 residues within 4Å: Chain B: D.109, G.110, C.112, C.115, C.123, E.124 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.109, B:C.112, B:C.115 ZN.12: 6 residues within 4Å: Chain C: C.54, T.56, H.79, D.168 Ligands: OCA.10, NAJ.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.54, C:H.79, C:D.168 ZN.13: 3 residues within 4Å: Chain C: D.332, H.334, R.345 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.332, C:D.332, C:H.334, H2O.38 ZN.14: 6 residues within 4Å: Chain C: D.109, G.110, C.112, C.115, C.123, E.124 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.109, C:C.112, C:C.115, C:C.123 ZN.17: 6 residues within 4Å: Chain D: C.54, T.56, H.79, D.168 Ligands: OCA.15, NAJ.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.54, D:H.79, D:D.168 ZN.18: 6 residues within 4Å: Chain D: D.109, G.110, C.112, C.115, C.123, E.124 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.109, D:C.112, D:C.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guy, J.E. et al., The structure of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix. J.Mol.Biol. (2003)

Release Date

2003-08-28

Peptides

ALCOHOL DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

ALCOHOL DEHYDROGENASE