SMTL ID : 3d70.1

Crystal structure of E253A mutant of BMRR bound to 22-bp oligonucleotide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

12 x IMD: IMIDAZOLE(Non-covalent)(Non-functional Binders)

IMD.1: 6 residues within 4Å: Chain A: L.148, N.149, Y.152, I.255 Ligands: IMD.3, GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.149 IMD.2: 7 residues within 4Å: Chain A: P.144, E.145, I.182, F.224, P.226, Y.229 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.226 IMD.3: 10 residues within 4Å: Chain A: V.147, Y.152, Y.170, A.172, Y.187, Y.229, A.253, I.255 Ligands: IMD.1, GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.152, A:Y.229 IMD.4: 3 residues within 4Å: Chain A: Y.5, Y.35 Ligands: IMD.6 No protein-ligand interaction detected (PLIP) IMD.5: 6 residues within 4Å: Chain A: T.166, N.167, N.168, Y.260 Chain C: S.58, Y.84 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.58, C:Y.84 IMD.6: 1 residues within 4Å: Ligands: IMD.4 No protein-ligand interaction detected (PLIP) IMD.10: 6 residues within 4Å: Chain C: L.148, N.149, Y.152, I.255 Ligands: IMD.12, GOL.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.149 IMD.11: 7 residues within 4Å: Chain C: P.144, E.145, I.182, F.224, P.226, Y.229 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.226 IMD.12: 10 residues within 4Å: Chain C: V.147, Y.152, Y.170, A.172, Y.187, Y.229, A.253, I.255 Ligands: IMD.10, GOL.18 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.152, C:Y.152 IMD.13: 3 residues within 4Å: Chain C: Y.5, Y.35 Ligands: IMD.15 No protein-ligand interaction detected (PLIP) IMD.14: 6 residues within 4Å: Chain A: S.58, Y.84 Chain C: T.166, N.167, N.168, Y.260 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.58, A:Y.84, A:Y.84, C:T.166 IMD.15: 1 residues within 4Å: Ligands: IMD.13 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: S.175, F.176, R.188, V.247, S.249, D.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.176, A:R.188 GOL.8: 6 residues within 4Å: Chain A: R.111, I.132, R.133, V.194, L.195, N.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.111, A:R.133, A:N.197, A:N.197 GOL.9: 5 residues within 4Å: Chain A: P.144, I.255 Ligands: IMD.1, IMD.2, IMD.3 No protein-ligand interaction detected (PLIP) GOL.16: 6 residues within 4Å: Chain C: S.175, F.176, R.188, V.247, S.249, D.250 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.176, C:R.188 GOL.17: 6 residues within 4Å: Chain C: R.111, I.132, R.133, V.194, L.195, N.197 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.111, C:R.133, C:N.197, C:N.197 GOL.18: 5 residues within 4Å: Chain C: P.144, I.255 Ligands: IMD.10, IMD.11, IMD.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newberry, K.J. et al., Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket and Transcription Activation through Tyrosine Expulsion. J.Biol.Chem. (2008)

Release Date

2008-08-26

Peptides

BMR promoter DNA: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

BMR promoter DNA