SMTL ID : 5owf.1

Structure of a LAO-binding protein mutant with glutamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: K.249, Y.251, F.252, D.253 Ligands: EDO.12 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: P.37, I.48, G.49, Y.251 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: D.106, D.232, T.236 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: A.111, D.112, K.207, D.208, K.209, F.212, G.213 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: T.31, D.32, T.33, T.34, S.71, D.72, N.163 Ligands: EDO.17 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: V.69, A.70, S.71, A.75, S.79 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: R.98, G.140, S.141, T.142, A.145 Ligands: GOL.22 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: I.94, Q.99, F.104, S.105, D.106, K.228 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: I.102, A.103, K.222 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: V.158, V.159, A.160 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: D.165, A.195 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: E.188, K.192, Y.251, F.252, D.253, F.254 Ligands: EDO.1 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: P.125, T.126, L.127, E.128, Y.146, W.151 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: S.187, K.192 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: D.241, T.243 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: R.239, Y.244, D.245, N.255, Y.257 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: D.72, N.163 Ligands: EDO.5 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: D.53, N.56, E.57, M.247 Ligand excluded by PLIP

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

PEG.19: 5 residues within 4Å: Chain A: V.159, Y.161, D.170, R.175, L.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.175, A:R.175

1 x GLN: GLUTAMINE(Non-covalent)

GLN.20: 12 residues within 4Å: Chain A: Y.35, F.73, S.90, S.91, L.92, S.93, R.98, K.138, S.141, T.142, Q.143, D.182 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:F.73 Hydrogen bonds: A:S.90, A:S.93, A:S.93, A:K.138, A:T.142 Water bridges: A:T.142, A:T.142 Salt bridges: A:R.98

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 6 residues within 4Å: Chain A: A.110, A.111, D.112, V.184, N.255, V.256 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.112, A:D.112, A:N.255, A:V.256 Water bridges: A:V.184 GOL.22: 8 residues within 4Å: Chain A: F.73, D.74, L.76, I.77, P.78, R.98, G.140 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.76, A:I.77, A:R.98, A:G.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banda-Vazquez, J. et al., Redesign of LAOBP to bind novel l-amino acid ligands. Protein Sci. (2018)

Release Date

2018-03-21

Peptides

Lysine/arginine/ornithine-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine/arginine/ornithine-binding periplasmic protein