SMTL ID : 7n5n.2 (1 other biounit)

PCNA from Thermococcus gammatolerans: crystal III, collection 15, 2.20 A, 28.7 MGy

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: K.176, K.183, R.212 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.176, A:K.183, A:R.212, A:R.212 GOL.2: 8 residues within 4Å: Chain A: V.62, Y.215, G.216, Y.219, L.259, A.260, P.261, R.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.216 GOL.3: 4 residues within 4Å: Chain A: T.48, E.49, E.50, P.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.49, A:E.49 GOL.4: 7 residues within 4Å: Chain A: K.100, T.122, A.123, R.125 Chain B: E.155, V.156, E.159 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.122, A:A.123, B:E.155, B:V.156 Water bridges: A:D.103, A:D.103 GOL.8: 3 residues within 4Å: Chain B: K.176, K.183, R.212 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.176, B:K.183, B:R.212, B:R.212 GOL.9: 8 residues within 4Å: Chain B: V.62, Y.215, G.216, Y.219, L.259, A.260, P.261, R.262 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.216 GOL.10: 4 residues within 4Å: Chain B: T.48, E.49, E.50, P.82 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.49, B:E.49 GOL.11: 7 residues within 4Å: Chain B: K.100, T.122, A.123, R.125 Chain C: E.155, V.156, E.159 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.122, B:A.123, C:E.155, C:V.156 Water bridges: B:D.103, B:D.103 GOL.15: 3 residues within 4Å: Chain C: K.176, K.183, R.212 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.176, C:K.183, C:R.212, C:R.212 GOL.16: 8 residues within 4Å: Chain C: V.62, Y.215, G.216, Y.219, L.259, A.260, P.261, R.262 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.216 GOL.17: 4 residues within 4Å: Chain C: T.48, E.49, E.50, P.82 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.49, C:E.49 GOL.18: 7 residues within 4Å: Chain A: E.155, V.156, E.159 Chain C: K.100, T.122, A.123, R.125 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:E.155, A:V.156, C:T.122, C:A.123 Water bridges: C:D.103, C:D.103

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

SO4.5: 2 residues within 4Å: Chain A: K.149, R.236 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.149, A:R.236 SO4.6: 2 residues within 4Å: Chain A: K.100, S.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.101 SO4.7: 5 residues within 4Å: Chain A: M.57, R.61, V.62, L.258, A.260 No protein-ligand interaction detected (PLIP) SO4.12: 2 residues within 4Å: Chain B: K.149, R.236 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.149, B:R.236 SO4.13: 2 residues within 4Å: Chain B: K.100, S.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.101 SO4.14: 5 residues within 4Å: Chain B: M.57, R.61, V.62, L.258, A.260 No protein-ligand interaction detected (PLIP) SO4.19: 2 residues within 4Å: Chain C: K.149, R.236 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.149, C:R.236 SO4.20: 2 residues within 4Å: Chain C: K.100, S.101 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.101 SO4.21: 5 residues within 4Å: Chain C: M.57, R.61, V.62, L.258, A.260 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marin-Tovar, Y. et al., PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation. Proteins (2022)

Release Date

2022-05-04

Peptides

DNA polymerase sliding clamp: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

DNA polymerase sliding clamp

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