SMTL ID : 8djq.1 (1 other biounit)

Sliding-clamp-DnaE1 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x GLN- PHE- ASP- LEU- PHE- GLY: DNA polymerase III subunit alpha peptide(Non-covalent)

GLN-PHE-ASP-LEU-PHE-GLY.1: 21 residues within 4Å: Chain A: L.162, T.179, R.181, F.182, R.183, L.184, P.257, L.262, N.334, Y.337, P.357, S.358, P.360, L.389, L.390, M.391, P.392, V.393, R.394 Ligands: ACE.3, NH2.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.179, A:R.181, A:F.182, A:L.184, A:P.257, A:L.262, A:L.389, A:R.394 Hydrogen bonds: A:R.181, A:M.391, A:P.392 Water bridges: A:N.334, A:N.334 GLN-PHE-ASP-LEU-PHE-GLY.2: 20 residues within 4Å: Chain B: L.162, T.179, R.181, F.182, R.183, L.184, P.257, L.262, N.334, Y.337, S.358, P.360, L.389, L.390, M.391, P.392, V.393, R.394 Ligands: ACE.5, NH2.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.179, B:R.181, B:F.182, B:L.184, B:P.257, B:L.262, B:L.389, B:R.394 Hydrogen bonds: B:R.181, B:R.181, B:R.181, B:M.391, B:P.392 Salt bridges: B:R.181

2 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.3: 4 residues within 4Å: Chain A: V.393, R.394 Ligands: GLN-PHE-ASP-LEU-PHE-GLY.1, GLN-PHE-ASP-LEU-PHE-GLY.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.394 ACE.5: 4 residues within 4Å: Chain B: V.393, R.394 Ligands: GLN-PHE-ASP-LEU-PHE-GLY.2, GLN-PHE-ASP-LEU-PHE-GLY.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.394 Hydrogen bonds: B:R.394

2 x NH2: AMINO GROUP(Non-functional Binders)

NH2.4: 3 residues within 4Å: Ligands: GLN-PHE-ASP-LEU-PHE-GLY.1, GLN-PHE-ASP-LEU-PHE-GLY.1, GLN-PHE-ASP-LEU-PHE-GLY.1 No protein-ligand interaction detected (PLIP) NH2.6: 3 residues within 4Å: Ligands: GLN-PHE-ASP-LEU-PHE-GLY.2, GLN-PHE-ASP-LEU-PHE-GLY.2, GLN-PHE-ASP-LEU-PHE-GLY.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kapur, M.K. et al., Interaction of the sliding clamp with mycobacterial polymerases. To Be Published

Release Date

2023-01-18

Peptides

Beta sliding clamp: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Beta sliding clamp

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