SMTL ID : 8dk9.1 (1 other biounit)

Sliding-clamp-DinX peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x GLN- GLU- SER- LEU- PHE- ALA: DNA polymerase IV 1 peptide(Non-covalent)

GLN-GLU-SER-LEU-PHE-ALA.1: 20 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, S.358, P.360, L.389, L.390, M.391, P.392, V.393, R.394 Ligands: ACE.7, NH2.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.162, A:T.179, A:R.181, A:F.182, A:L.184, A:P.257, A:P.257, A:L.262, A:P.360, A:L.389, A:M.391 Hydrogen bonds: A:R.181, A:R.181, A:M.391, A:P.392 Salt bridges: A:R.394 GLN-GLU-SER-LEU-PHE-ALA.2: 19 residues within 4Å: Chain B: T.179, R.181, F.182, R.183, L.184, P.257, F.259, L.262, N.334, Y.337, P.360, L.389, L.390, M.391, P.392, V.393, R.394 Ligands: ACE.9, NH2.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.179, B:F.182, B:L.184, B:P.257, B:P.257, B:L.262, B:P.360, B:M.391 Hydrogen bonds: B:R.181, B:R.181, B:R.181, B:R.181, B:M.391, B:P.392 Water bridges: B:N.334

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: R.166, A.201, K.258 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.166, A:R.166, A:E.255, A:K.258, A:K.258 Salt bridges: A:R.166, A:K.258 SO4.4: 2 residues within 4Å: Chain B: R.173, R.260 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.173, B:R.260 SO4.5: 4 residues within 4Å: Chain B: R.166, A.201, E.255, F.256 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.166, B:A.254, B:E.255 Salt bridges: B:R.166

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain B: K.258, F.259, R.260 Ligand excluded by PLIP

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

ACE.7: 4 residues within 4Å: Chain A: V.393, R.394 Ligands: GLN-GLU-SER-LEU-PHE-ALA.1, GLN-GLU-SER-LEU-PHE-ALA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.394 ACE.9: 4 residues within 4Å: Chain B: V.393, R.394 Ligands: GLN-GLU-SER-LEU-PHE-ALA.2, GLN-GLU-SER-LEU-PHE-ALA.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.394

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

NH2.8: 1 residues within 4Å: Ligands: GLN-GLU-SER-LEU-PHE-ALA.1 No protein-ligand interaction detected (PLIP) NH2.10: 3 residues within 4Å: Chain B: R.181 Ligands: GLN-GLU-SER-LEU-PHE-ALA.2, GLN-GLU-SER-LEU-PHE-ALA.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kapur, M.K. et al., Interaction of 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
A

B
B

Beta sliding clamp

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