SMTL ID : 6ptr.1

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Bartonella birtlesii bound to griselimycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-2-2-mer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: G.73, A.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.74 Water bridges: A:H.8, A:A.74 EDO.2: 3 residues within 4Å: Chain A: D.150, C.151, Q.345 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.345, A:D.366, A:Y.374 EDO.3: 7 residues within 4Å: Chain A: L.57, D.58, E.60, S.129, K.237, T.248, K.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.60, A:S.129, A:K.250 Water bridges: A:K.250 EDO.4: 5 residues within 4Å: Chain A: A.295, K.297, V.308, V.309, N.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.295, A:N.310, A:N.310 EDO.5: 3 residues within 4Å: Chain A: S.143, K.144, H.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.143, A:K.144 Water bridges: A:S.141 EDO.13: 7 residues within 4Å: Chain C: L.57, D.58, E.60, S.129, K.237, T.248, K.250 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.58, C:E.60, C:S.129, C:K.237 Water bridges: C:T.248

11 x IOD: IODIDE ION(Non-functional Binders)

IOD.6: 2 residues within 4Å: Chain A: R.294, A.295 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: R.380 Chain B: V.2, P.3 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: S.234 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: P.36, I.37 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: S.141, K.144 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: R.294, N.335 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: R.162, Y.164, L.165 Chain B: X.10 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain C: P.205, S.234 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain C: I.124 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain C: S.141 Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain C: R.294, A.295, N.335 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edwards, T.E. et al., Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Bartonella birtlesii bound to griselimycin. To Be Published

Release Date

2019-08-07

Peptides

Beta sliding clamp: AC
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
X

D
Y

Beta sliding clamp

ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY

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