SMTL ID : 4cvm.1

PaMurF in complex with AMP-PNP and UDP-MurNAc-tripeptide (mDAP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x ALA: ALANINE(Non-covalent)

ALA.1: 8 residues within 4Å: Chain A: N.140, L.141, N.142, N.143, L.145, G.146 Ligands: MUB.3, FGA.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.141, A:L.145 Hydrogen bonds: A:N.142, A:N.143, A:G.146

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 13 residues within 4Å: Chain A: T.30, D.31, S.32, R.33, F.41, L.44, G.46, P.47, R.48, F.49, G.51, Y.54 Ligands: MUB.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.49 Hydrogen bonds: A:D.31, A:S.32, A:S.32, A:R.33, A:R.48, A:F.49 Water bridges: A:T.30, A:T.30, A:D.31, A:R.33, A:L.44, A:L.44 Salt bridges: A:R.33 pi-Stacking: A:Y.54 pi-Cation interactions: A:R.33

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

MUB.3: 6 residues within 4Å: Chain A: R.33, N.143, L.145 Ligands: ALA.1, UDP.2, FGA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.143, A.1 Water bridges: A:D.31 Salt bridges: A:R.33

1 x FGA: GAMMA-D-GLUTAMIC ACID(Non-covalent)

FGA.4: 5 residues within 4Å: Chain A: N.140, N.142, N.143 Ligands: ALA.1, MUB.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.5: 16 residues within 4Å: Chain A: S.110, S.111, G.112, K.113, T.114, T.115, N.140, N.142, E.164, N.189, T.192, H.288, N.292, A.349 Ligands: MG.6, MG.7 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.111, A:G.112, A:K.113, A:K.113, A:T.114, A:T.114, A:T.115, A:T.115, A:N.140, A:N.140, A:N.142, A:E.164, A:N.189, A:N.292, A:N.292 Water bridges: A:S.110 pi-Cation interactions: A:H.288

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: T.114, N.140 Ligands: ANP.5, MG.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.114 MG.7: 5 residues within 4Å: Chain A: T.114, N.140, E.164 Ligands: ANP.5, MG.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.114, A:E.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majce, V. et al., Pamurf in Complex with AMP-Pnp and Udp-Murnac-Tripeptide. To be Published

Release Date

2015-04-22

Peptides

UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D- ALANINE LIGASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D- ALANINE LIGASE

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