SMTL ID : 4k3m.1

E.coli sliding clamp in complex with AcALDLF peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

1 x ASP- LEU- PHE: ALDLF(Non-covalent)

ASP-LEU-PHE.1: 12 residues within 4Å: Chain A: R.152, L.155, T.172, G.174, H.175, R.176, L.177, P.242, V.247, S.346, V.360, M.362 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.155, A:T.172, A:L.177, A:P.242, A:P.242, A:V.360 Hydrogen bonds: A:G.174 Water bridges: A:R.152, A:R.152 Salt bridges: A:R.152, A:H.175

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 6 residues within 4Å: Chain A: A.86, E.87, A.89, R.100, S.101, G.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.87, A:G.102 Water bridges: A:G.85, A:S.101 PEG.11: 8 residues within 4Å: Chain B: V.17, G.46, T.47, D.48, M.51, E.52, M.53, E.202 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.17, B:D.48 PEG.13: 8 residues within 4Å: Chain A: K.74, D.77 Chain B: A.271, I.272, S.274, N.275, E.276, R.279 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.275, B:R.279, A:D.77, A:D.77

7 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain A: G.280, A.294, N.295 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.280 CA.6: 3 residues within 4Å: Chain A: S.181, Q.355, S.356 No protein-ligand interaction detected (PLIP) CA.7: 1 residues within 4Å: Chain B: D.211 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.211 CA.8: 5 residues within 4Å: Chain B: E.161, T.162, E.163, S.190, H.191 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.161, B:T.162, H2O.21 CA.9: 2 residues within 4Å: Chain B: E.84, G.85 No protein-ligand interaction detected (PLIP) CA.14: 2 residues within 4Å: Chain B: E.163, E.166 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.163, H2O.24, H2O.24

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 6 residues within 4Å: Chain A: H.9, T.41, R.56, V.57, A.58, D.229 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.56, A:R.56, A:A.58 Water bridges: A:A.58, A:V.60 PGE.12: 3 residues within 4Å: Chain B: Y.284, K.291, E.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.291

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.10: 4 residues within 4Å: Chain B: D.121, W.122, Q.217, R.224 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.224, B:R.224 Water bridges: B:S.124, B:Q.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp. J.Med.Chem. (2013)

Release Date

2013-05-01

Peptides

DNA polymerase III subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA polymerase III subunit beta

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