SMTL ID : 6y1c.1

X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant D54F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-tetramer

Ligands

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: P.64, F.65, Q.68, K.89, A.90 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.68, A:Q.68, A:K.89 PEG.7: 5 residues within 4Å: Chain B: P.64, F.65, Q.68, K.89, A.90 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.68 Water bridges: B:K.89 PEG.8: 7 residues within 4Å: Chain B: E.213, S.217, G.225, H.226, I.227 Ligands: EDO.11, EDO.15 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.217, B:G.225, B:I.227 Water bridges: B:K.202, B:I.227, B:G.228 PEG.9: 5 residues within 4Å: Chain B: A.104, E.155, L.163, Y.166, Y.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.155 PEG.16: 5 residues within 4Å: Chain C: P.64, F.65, Q.68, K.89, A.90 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Q.68, C:Q.68, C:K.89 PEG.22: 5 residues within 4Å: Chain D: P.64, F.65, Q.68, K.89, A.90 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.68 Water bridges: D:K.89 PEG.23: 7 residues within 4Å: Chain D: E.213, S.217, G.225, H.226, I.227 Ligands: EDO.26, EDO.30 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.213, D:S.217, D:G.225, D:I.227 Water bridges: D:K.202, D:I.227, D:G.228 PEG.24: 5 residues within 4Å: Chain D: A.104, E.155, L.163, Y.166, Y.200 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.155, D:E.155

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: R.49, I.103, A.104, A.115, E.116, K.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.119 Water bridges: A:E.116 PG4.17: 6 residues within 4Å: Chain C: R.49, I.103, A.104, A.115, E.116, K.119 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.119

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

EDO.3: 3 residues within 4Å: Chain A: L.163, Y.166, Y.200 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.166, A:P.198, A:G.199 EDO.4: 5 residues within 4Å: Chain A: G.145, A.146, D.190, V.191, R.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.146, A:R.192 Water bridges: A:D.190 EDO.10: 6 residues within 4Å: Chain B: S.12, R.14, E.244 Chain D: S.12, R.14, E.40 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:S.12, B:S.12, D:S.12, D:R.14 Water bridges: D:E.40 EDO.11: 3 residues within 4Å: Chain B: E.213, E.214 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.214 EDO.13: 3 residues within 4Å: Chain B: S.60, V.61, G.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.60 Water bridges: B:Q.66 EDO.14: 5 residues within 4Å: Chain B: V.38, G.41, A.42, K.43, Q.66 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.43, B:Q.66, B:Q.66 EDO.15: 2 residues within 4Å: Chain B: H.226 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.226 EDO.18: 3 residues within 4Å: Chain C: L.163, Y.166, Y.200 3 PLIP interactions: 3 interactions with chain C Water bridges: C:P.198, C:G.199, C:Y.200 EDO.19: 5 residues within 4Å: Chain C: G.145, A.146, D.190, V.191, R.192 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.146, C:D.190, C:R.192 Water bridges: C:D.190 EDO.25: 6 residues within 4Å: Chain B: S.12, R.14, E.40 Chain D: S.12, R.14, E.244 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:S.12, D:S.12, B:S.12, B:R.14 EDO.26: 3 residues within 4Å: Chain D: E.213, E.214 Ligands: PEG.23 No protein-ligand interaction detected (PLIP) EDO.28: 3 residues within 4Å: Chain D: S.60, V.61, G.62 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.60 Water bridges: D:Q.66 EDO.29: 5 residues within 4Å: Chain D: V.38, G.41, A.42, K.43, Q.66 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.43, D:Q.66, D:Q.66 EDO.30: 2 residues within 4Å: Chain D: H.226 Ligands: PEG.23 1 PLIP interactions: 1 interactions with chain D Water bridges: D:H.226

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: Q.262 Chain D: Q.262 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: A:Q.262, D:Q.262, H2O.3, H2O.6, H2O.6, H2O.7 MG.20: 2 residues within 4Å: Chain B: Q.262 Chain C: Q.262 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.26, H2O.28, H2O.29, H2O.29

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 5 residues within 4Å: Chain A: T.26, G.48, R.49, H.50, V.53 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain C: T.26, G.48, R.49, H.50, V.53 Ligand excluded by PLIP

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 9 residues within 4Å: Chain B: G.145, A.146, C.184, A.185, D.188, Y.189, D.190, V.191, R.192 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.146, B:Y.189, B:D.190, B:V.191, B:R.192 Water bridges: B:A.185 PGE.27: 9 residues within 4Å: Chain D: G.145, A.146, C.184, A.185, D.188, Y.189, D.190, V.191, R.192 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:A.146, D:Y.189, D:D.190, D:D.190, D:V.191, D:R.192 Water bridges: D:A.185, D:D.188

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
B

C
A

D
B

R-specific alcohol dehydrogenase