SMTL ID : 7n5i.2 (1 other biounit)

PCNA from Thermococcus gammatolerans: crystal I, collection 1, 1.95 A, 5.22 MGy

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: K.176, K.183, R.212 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.176, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.216, A:R.262 GOL.3: 5 residues within 4Å: Chain A: T.48, E.50, G.51, N.68, P.70 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.48, A:G.51, A:N.68 Water bridges: A:T.48 GOL.4: 5 residues within 4Å: Chain A: E.155, K.158, K.162 Chain B: R.98, K.100 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.98, B:R.98, B:K.100, B:K.100 Water bridges: A:K.162 GOL.5: 6 residues within 4Å: Chain A: A.44, T.84, I.85, G.86, D.133, V.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.134, A:V.134 Water bridges: A:G.86 GOL.10: 3 residues within 4Å: Chain B: K.176, K.183, R.212 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.176, B:K.176, B:K.183, B:R.212, B:R.212 GOL.11: 8 residues within 4Å: Chain B: V.62, Y.215, G.216, Y.219, L.259, A.260, P.261, R.262 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.216, B:R.262 GOL.12: 5 residues within 4Å: Chain B: T.48, E.50, G.51, N.68, P.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.48, B:G.51, B:N.68 Water bridges: B:T.48 GOL.13: 5 residues within 4Å: Chain B: E.155, K.158, K.162 Chain C: R.98, K.100 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.98, C:R.98, C:K.100, C:K.100 Water bridges: B:K.162 GOL.14: 6 residues within 4Å: Chain B: A.44, T.84, I.85, G.86, D.133, V.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.134, B:V.134 Water bridges: B:G.86 GOL.19: 3 residues within 4Å: Chain C: K.176, K.183, R.212 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.176, C:K.176, C:K.183, C:R.212, C:R.212 GOL.20: 8 residues within 4Å: Chain C: V.62, Y.215, G.216, Y.219, L.259, A.260, P.261, R.262 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.216, C:R.262 GOL.21: 5 residues within 4Å: Chain C: T.48, E.50, G.51, N.68, P.70 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.48, C:G.51, C:N.68 Water bridges: C:T.48 GOL.22: 5 residues within 4Å: Chain A: R.98, K.100 Chain C: E.155, K.158, K.162 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Water bridges: C:K.162 Hydrogen bonds: A:R.98, A:R.98, A:K.100, A:K.100 GOL.23: 6 residues within 4Å: Chain C: A.44, T.84, I.85, G.86, D.133, V.134 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.134, C:V.134 Water bridges: C:G.86

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

SO4.6: 3 residues within 4Å: Chain A: K.149, R.236 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.149, A:R.236 SO4.7: 6 residues within 4Å: Chain A: F.146, T.147, K.149, E.206, E.208 Ligands: SO4.6 No protein-ligand interaction detected (PLIP) SO4.8: 3 residues within 4Å: Chain A: K.27, K.100, S.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.101 SO4.9: 7 residues within 4Å: Chain A: M.57, R.61, V.62, V.63, L.64, L.258, A.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.64, A:A.260 SO4.15: 3 residues within 4Å: Chain B: K.149, R.236 Ligands: SO4.16 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.149, B:R.236 SO4.16: 6 residues within 4Å: Chain B: F.146, T.147, K.149, E.206, E.208 Ligands: SO4.15 No protein-ligand interaction detected (PLIP) SO4.17: 3 residues within 4Å: Chain B: K.27, K.100, S.101 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.101 SO4.18: 7 residues within 4Å: Chain B: M.57, R.61, V.62, V.63, L.64, L.258, A.260 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.64, B:A.260 SO4.24: 3 residues within 4Å: Chain C: K.149, R.236 Ligands: SO4.25 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.149, C:R.236 SO4.25: 6 residues within 4Å: Chain C: F.146, T.147, K.149, E.206, E.208 Ligands: SO4.24 No protein-ligand interaction detected (PLIP) SO4.26: 3 residues within 4Å: Chain C: K.27, K.100, S.101 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.101 SO4.27: 7 residues within 4Å: Chain C: M.57, R.61, V.62, V.63, L.64, L.258, A.260 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.64, C:A.260

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
D

B
D

C
D

DNA polymerase sliding clamp

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