SMTL ID : 4wkm.4 (3 other biounits)

AmpR effector binding domain from Citrobacter freundii bound to UDP-MurNAc-pentapeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x ALA- FGA- API- DAL- DAL: ALA-FGA-API-DAL-DAL(Non-covalent)

ALA-FGA-API-DAL-DAL.1: 22 residues within 4Å: Chain A: V.19, T.21, N.49, N.50, R.51, R.64, Y.65, W.70, A.81, S.109, Y.110, R.111, F.136, D.137, S.138, S.139, M.142, P.156, Y.182 Chain B: E.57 Ligands: GOL.3, MUB.5 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.51, A:Y.65, A:Y.110, A:P.156 Hydrogen bonds: A:N.49, A:N.50, A:W.70, A:Y.110, A:R.111, A:R.111, A:S.139, A:S.139, A:Y.182, B:E.57 Water bridges: A:R.64, A:R.64, A:R.64, A:R.64, A:S.109, A:S.139, B:E.57 Salt bridges: A:R.64 ALA-FGA-API-DAL-DAL.2: 22 residues within 4Å: Chain A: E.57 Chain B: V.19, T.21, N.49, N.50, R.51, Y.65, W.70, A.81, M.83, S.109, Y.110, R.111, F.136, D.137, S.138, S.139, M.142, P.156, Y.182 Ligands: GOL.4, MUB.6 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.51, B:Y.65, B:Y.110, B:P.156 Hydrogen bonds: B:T.21, B:N.49, B:N.50, B:W.70, B:Y.110, B:R.111, B:R.111, B:S.139, B:S.139, B:Y.182, B:Y.182, A:E.57 Water bridges: B:R.51, B:R.51, B:R.64, B:S.139 Salt bridges: B:R.51, B:R.64

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Y.65, G.66, G.67, G.68, A.69, W.70, R.111 Ligands: ALA-FGA-API-DAL-DAL.1, ALA-FGA-API-DAL-DAL.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.67, A:A.69, A:A.69, A:R.111, A:R.111 Water bridges: A:Y.65, A:W.70 GOL.4: 8 residues within 4Å: Chain B: G.66, G.67, G.68, A.69, W.70, R.111 Ligands: ALA-FGA-API-DAL-DAL.2, ALA-FGA-API-DAL-DAL.2 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.67, B:A.69, B:R.111, B:R.111 Water bridges: B:G.66, B:W.70, B:W.70

2 x MUB: N-acetyl-alpha-muramic acid(Non-covalent)

MUB.5: 5 residues within 4Å: Chain A: Y.110, R.111 Ligands: ALA-FGA-API-DAL-DAL.1, ALA-FGA-API-DAL-DAL.1, ALA-FGA-API-DAL-DAL.1 No protein-ligand interaction detected (PLIP) MUB.6: 5 residues within 4Å: Chain B: Y.110, R.112 Ligands: ALA-FGA-API-DAL-DAL.2, ALA-FGA-API-DAL-DAL.2, ALA-FGA-API-DAL-DAL.2 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vadlamani, G. et al., The beta-Lactamase Gene Regulator AmpR Is a Tetramer That Recognizes and Binds the d-Ala-d-Ala Motif of Its Repressor UDP-N-acetylmuramic Acid (MurNAc)-pentapeptide. J.Biol.Chem. (2015)

Release Date

2014-12-17

Peptides

LysR family transcriptional regulator: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

LysR family transcriptional regulator

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