SMTL ID : 6y10.1

X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant Q126H

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-tetramer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: Q.262 Chain D: Q.262 Ligands: MG.37 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: D:Q.262, A:Q.262, H2O.3, H2O.8, H2O.50, H2O.55 MG.10: 5 residues within 4Å: Chain A: T.26, G.48, R.49, H.50, V.53 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain A: T.220 Chain D: T.220 Ligands: EDO.4, EDO.40, MG.47 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:T.220, D:T.220 MG.12: 5 residues within 4Å: Chain A: K.178, G.250, S.251 Chain C: T.260, A.261 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.260, H2O.37 MG.13: 3 residues within 4Å: Chain B: Q.262 Chain C: Q.262 Ligands: MG.25 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: C:Q.262, B:Q.262, H2O.19, H2O.23, H2O.35, H2O.39 MG.22: 5 residues within 4Å: Chain B: T.26, G.48, R.49, H.50, V.53 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain B: T.220 Chain C: T.220 Ligands: EDO.16, EDO.28, MG.35 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:T.220, B:T.220 MG.24: 5 residues within 4Å: Chain B: K.178, G.250, S.251 Chain D: T.260, A.261 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.260, H2O.53 MG.25: 3 residues within 4Å: Chain B: Q.262 Chain C: Q.262 Ligands: MG.13 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: C:Q.262, B:Q.262, H2O.19, H2O.23, H2O.35, H2O.39 MG.34: 5 residues within 4Å: Chain C: T.26, G.48, R.49, H.50, V.53 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain B: T.220 Chain C: T.220 Ligands: EDO.16, MG.23, EDO.28 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:T.220, B:T.220 MG.36: 5 residues within 4Å: Chain A: T.260, A.261 Chain C: K.178, G.250, S.251 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.260, H2O.6 MG.37: 3 residues within 4Å: Chain A: Q.262 Chain D: Q.262 Ligands: MG.1 6 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: D:Q.262, A:Q.262, H2O.3, H2O.8, H2O.50, H2O.55 MG.46: 5 residues within 4Å: Chain D: T.26, G.48, R.49, H.50, V.53 No protein-ligand interaction detected (PLIP) MG.47: 5 residues within 4Å: Chain A: T.220 Chain D: T.220 Ligands: EDO.4, MG.11, EDO.40 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Metal complexes: A:T.220, D:T.220 MG.48: 5 residues within 4Å: Chain B: T.260, A.261 Chain D: K.178, G.250, S.251 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.260, H2O.22

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

EDO.2: 6 residues within 4Å: Chain A: E.77, W.80, T.81, F.130, R.133, L.134 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: E.55, K.56 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: T.220, K.221, Y.259 Chain D: Q.262 Ligands: MG.11, EDO.40, MG.47 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: C.184, A.185, Y.189, D.190, V.191 Chain C: M.224 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.118, L.121 Chain B: D.126 Ligands: EDO.18 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: E.214, Q.218 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: E.155, L.163, Y.166, Y.200 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: K.89, A.90, F.91, G.92 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: E.77, W.80, T.81, F.130, R.133, L.134 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain B: E.55, K.56 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: T.220, K.221, Y.259 Chain C: Q.262 Ligands: MG.23, EDO.28, MG.35 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: C.184, A.185, Y.189, D.190, V.191 Chain D: M.224 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: D.126 Chain B: R.118, L.121 Ligands: EDO.6 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: E.214, Q.218 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: E.155, L.163, Y.166, Y.200 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: K.89, A.90, F.91, G.92 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain C: E.77, W.80, T.81, F.130, R.133, L.134 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain C: E.55, K.56 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: Q.262 Chain C: T.220, K.221, Y.259 Ligands: EDO.16, MG.23, MG.35 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: M.224 Chain C: C.184, A.185, Y.189, D.190, V.191 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: R.118, L.121 Chain D: D.126 Ligands: EDO.42 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain C: E.214, Q.218 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: E.155, L.163, Y.166, Y.200 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain C: K.89, A.90, F.91, G.92 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain D: E.77, W.80, T.81, F.130, R.133, L.134 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain D: E.55, K.56 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain A: Q.262 Chain D: T.220, K.221, Y.259 Ligands: EDO.4, MG.11, MG.47 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: M.224 Chain D: C.184, A.185, Y.189, D.190, V.191 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain C: D.126 Chain D: R.118, L.121 Ligands: EDO.30 Ligand excluded by PLIP EDO.43: 2 residues within 4Å: Chain D: E.214, Q.218 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain D: E.155, L.163, Y.166, Y.200 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain D: K.89, A.90, F.91, G.92 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hermann, J. et al., Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts. Crystals (2021)

Release Date

2020-02-19

Peptides

R-specific alcohol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

R-specific alcohol dehydrogenase