SMTL ID : 7n5m.1 (1 other biounit)

PCNA from Thermococcus gammatolerans: crystal III, collection 1, 2.00 A, 1.91 MGy

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: I.174, K.176, K.183, R.212 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.176, A:K.176, 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: 7 residues within 4Å: Chain A: T.48, E.50, G.51, V.52, S.53, N.68, P.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.53, A:N.68 Water bridges: A:E.71 GOL.4: 7 residues within 4Å: Chain A: A.44, T.84, I.85, G.86, I.132, D.133, V.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.85, A:V.134, A:E.136, A:E.136 Water bridges: A:G.86 GOL.10: 4 residues within 4Å: Chain B: I.174, K.176, K.183, R.212 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.176, B:K.176, 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: 7 residues within 4Å: Chain B: T.48, E.50, G.51, V.52, S.53, N.68, P.70 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.53, B:N.68 Water bridges: B:E.71 GOL.13: 7 residues within 4Å: Chain B: A.44, T.84, I.85, G.86, I.132, D.133, V.134 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.85, B:V.134, B:E.136, B:E.136 Water bridges: B:G.86 GOL.19: 4 residues within 4Å: Chain C: I.174, K.176, K.183, R.212 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.176, C:K.176, 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: 7 residues within 4Å: Chain C: T.48, E.50, G.51, V.52, S.53, N.68, P.70 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.53, C:N.68 Water bridges: C:E.71 GOL.22: 7 residues within 4Å: Chain C: A.44, T.84, I.85, G.86, I.132, D.133, V.134 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.85, C:V.134, C:E.136, C:E.136 Water bridges: C:G.86

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

SO4.5: 3 residues within 4Å: Chain A: K.149, R.236 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.149, A:R.236 SO4.6: 6 residues within 4Å: Chain A: F.146, T.147, A.148, K.149, E.206 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.206 SO4.7: 3 residues within 4Å: Chain A: K.27, K.100, S.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.101 Water bridges: A:K.102 Salt bridges: A:K.100 SO4.8: 7 residues within 4Å: Chain A: M.57, R.61, V.62, L.64, P.242, L.258, A.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.62, A:L.64 SO4.9: 3 residues within 4Å: Chain A: K.158, K.162, K.229 9 PLIP interactions: 9 interactions with chain A Water bridges: A:K.158, A:K.158, A:K.158, A:K.162, A:K.162, A:K.225 Salt bridges: A:K.158, A:K.162, A:K.229 SO4.14: 3 residues within 4Å: Chain B: K.149, R.236 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.149, B:R.236 SO4.15: 6 residues within 4Å: Chain B: F.146, T.147, A.148, K.149, E.206 Ligands: SO4.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.206 SO4.16: 3 residues within 4Å: Chain B: K.27, K.100, S.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.101 Water bridges: B:K.102 Salt bridges: B:K.100 SO4.17: 7 residues within 4Å: Chain B: M.57, R.61, V.62, L.64, P.242, L.258, A.260 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.62, B:L.64 SO4.18: 3 residues within 4Å: Chain B: K.158, K.162, K.229 9 PLIP interactions: 9 interactions with chain B Water bridges: B:K.158, B:K.158, B:K.158, B:K.162, B:K.162, B:K.225 Salt bridges: B:K.158, B:K.162, B:K.229 SO4.23: 3 residues within 4Å: Chain C: K.149, R.236 Ligands: SO4.24 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.149, C:R.236 SO4.24: 6 residues within 4Å: Chain C: F.146, T.147, A.148, K.149, E.206 Ligands: SO4.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.206 SO4.25: 3 residues within 4Å: Chain C: K.27, K.100, S.101 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.101 Water bridges: C:K.102 Salt bridges: C:K.100 SO4.26: 7 residues within 4Å: Chain C: M.57, R.61, V.62, L.64, P.242, L.258, A.260 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.62, C:L.64 SO4.27: 3 residues within 4Å: Chain C: K.158, K.162, K.229 9 PLIP interactions: 9 interactions with chain C Water bridges: C:K.158, C:K.158, C:K.158, C:K.162, C:K.162, C:K.225 Salt bridges: C:K.158, C:K.162, C:K.229

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
A

B
A

C
A

DNA polymerase sliding clamp

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