SMTL ID : 6drt.1

Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-3-3-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: L.127, M.184, A.185, M.187, K.188 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.131, A:R.131 EDO.2: 6 residues within 4Å: Chain B: G.132, L.133, Q.134, K.164 Chain C: W.92, P.93 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.132, B:K.164 EDO.3: 5 residues within 4Å: Chain B: L.127, S.130, M.184, M.187, K.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.127, B:S.130, B:A.185 EDO.4: 4 residues within 4Å: Chain C: P.108, F.109, L.197, K.208 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.208, C:K.208 EDO.5: 5 residues within 4Å: Chain C: F.109, P.110, V.111, W.199 Chain F: L.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.111, C:V.111 EDO.6: 6 residues within 4Å: Chain C: N.35, T.37, N.183, A.185, N.186 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.35, C:N.183 Water bridges: C:T.37, C:N.186 EDO.7: 8 residues within 4Å: Chain C: I.17, A.33, N.35, T.38, A.185, N.186, K.188 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.35, C:T.38, C:T.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, K. et al., T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction. Nucleic Acids Res. (2018)

Release Date

2018-09-26

Peptides

DNA polymerase clamp: ABC
GP45 recognition loop: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA polymerase clamp

GP45 recognition loop

Related Entries With Identical Sequence