SMTL ID : 6p74.1

OLD nuclease from Thermus Scotoductus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

4 x PT: PLATINUM (II) ION(Non-covalent)

PT.1: 3 residues within 4Å: Chain B: R.56 Ligands: PT.2, SO4.3 No protein-ligand interaction detected (PLIP) PT.2: 5 residues within 4Å: Chain A: C.12, G.31, T.36 Ligands: PT.1, SO4.3 No protein-ligand interaction detected (PLIP) PT.15: 3 residues within 4Å: Chain A: R.56 Ligands: PT.16, SO4.17 No protein-ligand interaction detected (PLIP) PT.16: 5 residues within 4Å: Chain B: C.12, G.31, T.36 Ligands: PT.15, SO4.17 No protein-ligand interaction detected (PLIP)

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

SO4.3: 10 residues within 4Å: Chain A: N.30, G.31, A.32, G.33, K.34, T.35, T.36 Chain B: Q.59 Ligands: PT.1, PT.2 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: M.1, L.2, F.76, D.77, P.78, H.132, A.133 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: G.126, T.127 Ligands: EPE.13 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: V.336, S.337, Y.338, R.340, A.421 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: P.29, R.327, K.328 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: Y.379, D.491 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: H.283, P.284, Q.285, R.288 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain A: W.49, P.50, V.103, D.104, L.105 Ligands: EPE.13 Ligand excluded by PLIP SO4.17: 10 residues within 4Å: Chain A: Q.59 Chain B: N.30, G.31, A.32, G.33, K.34, T.35, T.36 Ligands: PT.15, PT.16 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain B: M.1, L.2, F.76, D.77, P.78, H.132, A.133 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: G.126, T.127 Ligands: EPE.27 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain B: V.336, S.337, Y.338, R.340, A.421 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: P.29, R.327, K.328 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: Y.379, D.491 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: H.283, P.284, Q.285, R.288 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain B: W.49, P.50, V.103, D.104, L.105 Ligands: EPE.27 Ligand excluded by PLIP

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 6 residues within 4Å: Chain A: W.435, Q.449, S.478, E.480, A.481, R.487 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.478 Salt bridges: A:R.487 EPE.12: 9 residues within 4Å: Chain A: P.22, L.23, D.299, N.318, R.319, E.321, A.322, R.351, K.355 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.23 Salt bridges: A:D.299, A:E.321, A:E.321, A:R.351, A:K.355 EPE.13: 8 residues within 4Å: Chain A: W.49, V.125, G.126, T.127 Chain B: D.245, E.246 Ligands: SO4.5, SO4.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.246 pi-Cation interactions: A:W.49, A:W.49 EPE.25: 6 residues within 4Å: Chain B: W.435, Q.449, S.478, E.480, A.481, R.487 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.478 Salt bridges: B:R.487 EPE.26: 9 residues within 4Å: Chain B: P.22, L.23, D.299, N.318, R.319, E.321, A.322, R.351, K.355 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.23 Salt bridges: B:D.299, B:E.321, B:E.321, B:R.351, B:K.355 EPE.27: 8 residues within 4Å: Chain A: D.245, E.246 Chain B: W.49, V.125, G.126, T.127 Ligands: SO4.19, SO4.24 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A pi-Cation interactions: B:W.49, B:W.49 Hydrogen bonds: A:E.246

2 x SM: SAMARIUM (III) ION(Non-covalent)

SM.14: 2 residues within 4Å: Chain A: D.431, E.480 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.431, A:E.480, H2O.1, H2O.1, H2O.1 SM.28: 2 residues within 4Å: Chain B: D.431, E.480 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.431, B:E.480, H2O.3, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiltz, C.J. et al., The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases. Nucleic Acids Res. (2020)

Release Date

2020-01-29

Peptides

Putative ATP-dependent endonuclease of the OLD family: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative ATP-dependent endonuclease of the OLD family