SMTL ID : 3fpc.1

Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.37, S.39, H.59, D.150 Ligands: CAC.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.37, A:H.59, A:D.150 ZN.4: 5 residues within 4Å: Chain B: C.37, S.39, H.59, D.150 Ligands: CAC.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.37, B:H.59, B:D.150 ZN.11: 5 residues within 4Å: Chain C: C.37, S.39, H.59, D.150 Ligands: CAC.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.37, C:H.59, C:D.150 ZN.20: 5 residues within 4Å: Chain D: C.37, S.39, H.59, D.150 Ligands: CAC.21 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.37, D:H.59, D:D.150

4 x CAC: CACODYLATE ION(Non-covalent)

CAC.2: 11 residues within 4Å: Chain A: C.37, S.39, H.59, A.85, I.86, W.110, D.150, T.154, L.294 Chain C: M.285 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.39, A:T.154 CAC.5: 11 residues within 4Å: Chain B: C.37, S.39, H.59, A.85, I.86, W.110, D.150, T.154, L.294 Chain D: M.285 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.39, B:D.150 CAC.12: 12 residues within 4Å: Chain A: M.285 Chain C: C.37, S.39, H.59, A.85, I.86, W.110, D.150, T.154, L.294 Ligands: ZN.11, EDO.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.39, C:T.154 CAC.21: 12 residues within 4Å: Chain B: M.285 Chain D: C.37, S.39, H.59, A.85, I.86, W.110, D.150, T.154, L.294 Ligands: ZN.20, EDO.27 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.39

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 2 residues within 4Å: Chain A: N.163, K.238 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain A Water bridges: C:R.97, A:N.163, A:N.163, A:N.163, A:N.163 Hydrogen bonds: A:K.238, A:G.259

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain B: G.98, Y.99, H.100, Q.101, H.157 Chain D: H.287 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.98, B:H.100, B:Q.101, B:H.157 EDO.7: 3 residues within 4Å: Chain B: P.137, D.307, F.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.307 EDO.9: 5 residues within 4Å: Chain B: T.169, R.193 Chain C: D.307 Ligands: EDO.10, EDO.14 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.193 Water bridges: C:D.307, C:D.307, C:Y.311 EDO.10: 8 residues within 4Å: Chain B: T.169, K.234, G.235, V.236, D.237, K.257 Chain C: R.304 Ligands: EDO.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.169, B:G.235, B:K.257, C:R.304 EDO.14: 4 residues within 4Å: Chain C: P.137, D.307, F.310 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.307 Water bridges: C:Y.311 EDO.15: 8 residues within 4Å: Chain C: C.37, S.39, T.154, V.178, V.265, N.266, Y.267 Ligands: CAC.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.266, C:Y.267 EDO.16: 2 residues within 4Å: Chain C: D.272, N.273 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Water bridges: A:D.275 Hydrogen bonds: C:D.272, C:N.273 EDO.17: 5 residues within 4Å: Chain A: H.287 Chain C: Y.99, Q.101, H.157, P.296 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.101, C:Q.101 Water bridges: C:H.157 EDO.18: 3 residues within 4Å: Chain B: L.166 Chain C: R.301, R.304 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.301, C:R.301 Water bridges: D:Q.96 EDO.22: 6 residues within 4Å: Chain B: H.287 Chain D: G.98, Y.99, H.100, Q.101, H.157 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.98, D:H.100, D:Q.101, D:H.157 EDO.23: 6 residues within 4Å: Chain A: G.167, K.234 Chain D: L.300, E.303, R.304, D.307 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:K.234, A:K.234, D:D.307 Water bridges: A:T.169, A:K.257, D:D.307 EDO.24: 3 residues within 4Å: Chain D: P.137, D.307, F.310 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.307 EDO.25: 4 residues within 4Å: Chain A: L.166 Chain D: L.300, R.301, R.304 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:L.166, D:R.301 Water bridges: C:Q.96 EDO.27: 7 residues within 4Å: Chain D: C.37, T.38, S.39, V.178, V.265, Y.267 Ligands: CAC.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.39, D:V.265, D:Y.267

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.8: 4 residues within 4Å: Chain A: R.91 Chain B: F.25, R.91, D.128 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.91, B:D.128 Water bridges: B:D.128 NO3.26: 5 residues within 4Å: Chain C: F.25, R.91 Chain D: F.25, R.91, D.128 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.91, D:D.128 Water bridges: D:D.128

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.13: 5 residues within 4Å: Chain C: F.25, R.91, D.128 Chain D: F.25, R.91 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.128 Water bridges: C:R.91 pi-Stacking: C:F.25

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

NA.19: 6 residues within 4Å: Chain C: P.88, D.89, S.103, A.108, G.109, K.111 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.89, C:A.108, C:K.111 NA.28: 6 residues within 4Å: Chain D: P.88, D.89, S.103, A.108, G.109, K.111 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.89, D:A.108, D:K.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goihberg, E. et al., Biochemical and structural properties of chimeras constructed by exchange of cofactor-binding domains in alcohol dehydrogenases from thermophilic and mesophilic microorganisms. Biochemistry (2010)

Release Date

2010-01-19

Peptides

NADP-dependent alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NADP-dependent alcohol dehydrogenase