SMTL ID : 1d1s.1 (3 other biounits)

WILD-TYPE HUMAN SIGMA (CLASS IV) ALCOHOL DEHYDROGENASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

19 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.97, R.98, C.100, C.103, C.111, I.112 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.97, A:C.100, A:C.103, A:C.111 ZN.2: 5 residues within 4Å: Chain A: C.46, H.67, C.173 Ligands: ACT.7, NAD.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.46, A:H.67, A:C.173, ACT.7 ZN.3: 3 residues within 4Å: Chain A: H.270 Ligands: ACT.9, NAD.12 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.270, H2O.2 ZN.4: 3 residues within 4Å: Chain A: H.137 Ligands: ACT.8, ACT.10 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.137, ACT.8, ACT.10 ZN.5: 3 residues within 4Å: Chain B: H.270 Ligands: ACT.19, NAD.24 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.270, H2O.6 ZN.6: 3 residues within 4Å: Chain A: E.356, E.359, L.360 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.356, A:E.356, A:E.359, H2O.2 ZN.13: 5 residues within 4Å: Chain B: C.97, R.98, C.100, C.103, C.111 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.97, B:C.100, B:C.103, B:C.111 ZN.14: 5 residues within 4Å: Chain B: C.46, H.67, C.173 Ligands: ACT.18, NAD.24 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.46, B:H.67, B:C.173 ZN.15: 1 residues within 4Å: Chain B: H.137 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.137, H2O.6 ZN.16: 4 residues within 4Å: Chain B: D.340 Chain D: E.99 Ligands: ACT.36, ACT.37 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:E.99, D:E.99, B:D.340, B:D.340 ZN.17: 4 residues within 4Å: Chain B: E.16 Ligands: CAC.20, CAC.21, CAC.22 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.16, B:E.16 ZN.25: 6 residues within 4Å: Chain C: C.97, R.98, C.100, C.103, C.111, I.112 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.97, C:C.100, C:C.103, C:C.111 ZN.26: 5 residues within 4Å: Chain C: C.46, H.67, C.173 Ligands: ACT.28, NAD.30 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:C.46, C:H.67, C:C.173, ACT.28 ZN.27: 3 residues within 4Å: Chain C: H.270 Ligands: ACT.29, NAD.30 3 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:H.270, H2O.9, ACT.29 ZN.31: 5 residues within 4Å: Chain D: C.97, C.100, C.103, C.111, I.112 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.97, D:C.100, D:C.103, D:C.111 ZN.32: 5 residues within 4Å: Chain D: C.46, H.67, C.173 Ligands: ACT.38, NAD.41 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:C.46, D:H.67, D:C.173, ACT.38 ZN.33: 3 residues within 4Å: Chain D: H.270 Ligands: ACT.39, NAD.41 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.270, H2O.13 ZN.34: 2 residues within 4Å: Chain D: H.137 Ligands: ACT.40 4 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:H.137, H2O.12, H2O.14, ACT.40 ZN.35: 1 residues within 4Å: Chain D: H.347 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.347

13 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 8 residues within 4Å: Chain A: C.46, T.48, F.93, M.140, C.173, V.293 Ligands: ZN.2, NAD.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.93 Salt bridges: A:H.67 ACT.8: 5 residues within 4Å: Chain A: K.60, V.121, H.137 Ligands: ZN.4, ACT.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.121 Salt bridges: A:K.60, A:H.137 ACT.9: 4 residues within 4Å: Chain A: L.223, H.270 Ligands: ZN.3, NAD.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.223 Salt bridges: A:H.270 ACT.10: 4 residues within 4Å: Chain A: F.61, H.137 Ligands: ZN.4, ACT.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.61 Salt bridges: A:H.137 ACT.18: 9 residues within 4Å: Chain B: C.46, T.48, H.67, F.93, M.140, C.173, V.293 Ligands: ZN.14, NAD.24 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.93 Hydrogen bonds: B:T.48 Salt bridges: B:H.67 ACT.19: 4 residues within 4Å: Chain B: L.223, H.270 Ligands: ZN.5, NAD.24 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.270 Salt bridges: B:H.270 ACT.28: 9 residues within 4Å: Chain C: C.46, T.48, H.67, F.93, M.140, C.173, V.293 Ligands: ZN.26, NAD.30 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.93 Hydrogen bonds: C:T.48 Salt bridges: C:H.67 ACT.29: 3 residues within 4Å: Chain C: H.270 Ligands: ZN.27, NAD.30 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.270 ACT.36: 6 residues within 4Å: Chain B: D.340, D.342 Chain D: E.99, R.113 Ligands: ZN.16, ACT.37 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.99, B:D.342 Salt bridges: D:R.113 ACT.37: 5 residues within 4Å: Chain B: D.340 Chain D: K.34, E.99 Ligands: ZN.16, ACT.36 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:K.34 Hydrogen bonds: D:R.113 Salt bridges: D:K.34 ACT.38: 9 residues within 4Å: Chain D: C.46, T.48, H.67, F.93, M.140, C.173, V.293 Ligands: ZN.32, NAD.41 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.93 Hydrogen bonds: D:T.48 Salt bridges: D:H.67 ACT.39: 2 residues within 4Å: Chain D: H.270 Ligands: ZN.33 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.270 ACT.40: 3 residues within 4Å: Chain D: K.60, H.137 Ligands: ZN.34 3 PLIP interactions: 3 interactions with chain D Water bridges: D:K.60 Salt bridges: D:K.60, D:H.137

5 x CAC: CACODYLATE ION(Non-covalent)

CAC.11: 2 residues within 4Å: Chain A: M.232, A.236 No protein-ligand interaction detected (PLIP) CAC.20: 6 residues within 4Å: Chain B: E.16, F.61, P.62 Ligands: ZN.17, CAC.21, CAC.22 No protein-ligand interaction detected (PLIP) CAC.21: 4 residues within 4Å: Chain B: E.16 Ligands: ZN.17, CAC.20, CAC.22 No protein-ligand interaction detected (PLIP) CAC.22: 4 residues within 4Å: Chain B: E.16 Ligands: ZN.17, CAC.20, CAC.21 No protein-ligand interaction detected (PLIP) CAC.23: 5 residues within 4Å: Chain A: G.258, N.259 Chain B: C.100, N.101, I.112 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.101, A:N.259 Water bridges: B:A.102, A:H.282

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

NAD.12: 29 residues within 4Å: Chain A: R.47, T.48, H.51, C.173, T.177, G.198, L.199, G.200, G.201, V.202, D.222, L.223, K.227, V.267, I.268, G.269, H.270, V.291, G.292, V.293, C.316, V.317, F.318, R.368 Chain B: F.308 Ligands: ZN.2, ZN.3, ACT.7, ACT.9 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.177, A:V.202 Hydrogen bonds: A:R.47, A:T.48, A:H.51, A:L.199, A:G.201, A:V.202, A:L.223, A:K.227, A:K.227, A:I.268, A:V.293, A:C.316, A:F.318 Water bridges: A:R.47, A:R.47, A:G.200, A:G.203, A:R.368 Salt bridges: A:R.47, A:R.368 NAD.24: 33 residues within 4Å: Chain A: F.308 Chain B: C.46, R.47, T.48, H.51, C.173, T.177, G.198, L.199, G.200, G.201, V.202, G.203, D.222, L.223, K.227, V.267, I.268, G.269, H.270, T.273, V.291, G.292, V.293, C.316, V.317, F.318, L.361, R.368 Ligands: ZN.5, ZN.14, ACT.18, ACT.19 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.177, B:V.202 Hydrogen bonds: B:R.47, B:H.51, B:T.177, B:L.199, B:G.201, B:V.202, B:G.203, B:L.223, B:I.268, B:H.270, B:V.293, B:C.316, B:F.318 Water bridges: B:G.200, B:R.368 Salt bridges: B:R.47, B:R.368 NAD.30: 30 residues within 4Å: Chain C: R.47, T.48, H.51, C.173, T.177, G.198, L.199, G.200, G.201, V.202, D.222, L.223, N.224, K.227, V.267, I.268, G.269, H.270, V.291, G.292, V.293, C.316, V.317, F.318, R.368 Chain D: F.308 Ligands: ZN.26, ZN.27, ACT.28, ACT.29 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:T.177, C:V.202 Hydrogen bonds: C:R.47, C:H.51, C:L.199, C:L.199, C:G.201, C:V.202, C:G.203, C:L.223, C:K.227, C:K.227, C:I.268, C:V.293, C:C.316, C:F.318 Water bridges: C:G.200, C:G.200 Salt bridges: C:R.47, C:R.368 NAD.41: 28 residues within 4Å: Chain C: F.308 Chain D: R.47, T.48, H.51, C.173, T.177, G.198, L.199, G.200, G.201, V.202, D.222, L.223, K.227, V.267, I.268, G.269, H.270, V.291, G.292, V.293, C.316, V.317, F.318, R.368 Ligands: ZN.32, ZN.33, ACT.38 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:T.177, D:V.202 Hydrogen bonds: D:R.47, D:H.51, D:L.199, D:G.201, D:V.202, D:L.223, D:I.268, D:V.291, D:V.293, D:F.318 Water bridges: D:G.200, D:G.203, D:K.227, D:R.368 Salt bridges: D:R.47, D:K.227, D:R.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, P.T. et al., Methionine-141 directly influences the binding of 4-methylpyrazole in human sigma sigma alcohol dehydrogenase. Protein Sci. (1999)

Release Date

1999-09-29

Peptides

ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ALCOHOL DEHYDROGENASE CLASS IV SIGMA CHAIN

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