SMTL ID : 5im3.1

Crystal structure of the class I ribonucleotide reductase from Pseudomonas aeruginosa in complex with dATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

12 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 14 residues within 4Å: Chain A: V.34, K.36, R.37, P.43, Y.44, T.45, K.48, I.49, I.98, I.101, Q.102, Y.121 Ligands: DTP.2, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.49 Hydrogen bonds: A:P.43, A:T.45, A:Q.102 Salt bridges: A:K.36, A:K.36, A:R.37, A:K.55 DTP.2: 13 residues within 4Å: Chain A: R.37, A.52, K.55, A.56, A.59, Q.102, D.120, Y.121, Y.124, R.128, R.132 Ligands: DTP.1, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.121, A:Y.124 Hydrogen bonds: A:Q.102 Salt bridges: A:R.37, A:R.37, A:K.55, A:R.132, A:R.132 pi-Stacking: A:Y.124, A:Y.124 DTP.4: 12 residues within 4Å: Chain A: K.397, A.439, V.440 Chain B: D.380, D.381, L.382, I.385, V.409, R.410, I.416, K.417, F.429 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.385 Hydrogen bonds: B:D.380, B:L.382, B:R.410, B:K.417, A:V.440, A:N.441 Salt bridges: B:R.410, A:K.397, A:K.397 DTP.5: 13 residues within 4Å: Chain A: D.380, D.381, L.382, I.385, V.409, R.410, I.416, K.417, T.419, F.429 Chain B: K.397, A.439, V.440 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.385 Hydrogen bonds: A:D.380, A:L.382, A:K.417, A:T.419, B:V.440 Water bridges: A:D.381, A:S.383, A:R.410 Salt bridges: A:R.410, B:K.397, B:K.397 DTP.6: 17 residues within 4Å: Chain B: V.34, K.36, R.37, V.42, P.43, Y.44, T.45, K.48, I.49, A.52, I.98, I.101, Q.102, V.105, Y.121 Ligands: DTP.7, MG.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.49, B:I.101 Hydrogen bonds: B:P.43, B:T.45, B:Q.102 Salt bridges: B:K.36, B:K.36, B:R.37 DTP.7: 13 residues within 4Å: Chain B: R.37, A.52, K.55, A.56, A.59, Q.102, D.120, Y.121, Y.124, R.128, R.132 Ligands: DTP.6, MG.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.121, B:Y.124 Hydrogen bonds: B:Q.102, B:Y.121, B:R.128 Water bridges: B:R.37, B:R.37, B:R.37, B:R.37 Salt bridges: B:R.37, B:R.37, B:K.55, B:R.132, B:R.132 pi-Stacking: B:Y.124, B:Y.124 DTP.9: 14 residues within 4Å: Chain C: V.34, K.36, R.37, P.43, Y.44, T.45, K.48, I.49, I.98, I.101, Q.102, Y.121 Ligands: DTP.10, MG.11 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.49 Hydrogen bonds: C:P.43, C:T.45, C:T.45, C:Q.102, C:Y.121 Salt bridges: C:K.36, C:K.36, C:R.37, C:K.55 DTP.10: 13 residues within 4Å: Chain C: R.37, A.52, K.55, A.56, A.59, Q.102, D.120, Y.121, Y.124, R.128, R.132 Ligands: DTP.9, MG.11 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.121, C:Y.124 Hydrogen bonds: C:Q.102, C:Y.124 Salt bridges: C:R.37, C:R.37, C:K.55, C:R.132, C:R.132 pi-Stacking: C:Y.124, C:Y.124 DTP.12: 12 residues within 4Å: Chain C: K.397, A.439, V.440 Chain D: D.380, D.381, L.382, I.385, V.409, R.410, I.416, K.417, F.429 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.385 Hydrogen bonds: D:D.380, D:L.382, D:R.410, D:K.417, C:V.440, C:N.441 Salt bridges: D:R.410, C:K.397, C:K.397 DTP.13: 13 residues within 4Å: Chain C: D.380, D.381, L.382, I.385, V.409, R.410, I.416, K.417, T.419, F.429 Chain D: K.397, A.439, V.440 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.385 Hydrogen bonds: C:D.380, C:L.382, C:K.417, D:V.440 Water bridges: C:S.383, C:S.383, C:R.410 Salt bridges: C:R.410, D:K.397, D:K.397 DTP.14: 17 residues within 4Å: Chain D: V.34, K.36, R.37, V.42, P.43, Y.44, T.45, K.48, I.49, A.52, I.98, I.101, Q.102, V.105, Y.121 Ligands: DTP.15, MG.16 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.49, D:I.101 Hydrogen bonds: D:P.43, D:T.45, D:Q.102, D:Y.121 Salt bridges: D:K.36, D:K.36, D:R.37 DTP.15: 13 residues within 4Å: Chain D: R.37, A.52, K.55, A.56, A.59, Q.102, D.120, Y.121, Y.124, R.128, R.132 Ligands: DTP.14, MG.16 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:Y.121, D:Y.124 Hydrogen bonds: D:Q.102, D:Y.124, D:R.128 Water bridges: D:R.37, D:R.37, D:R.37, D:R.37 Salt bridges: D:R.37, D:R.37, D:K.55, D:R.132, D:R.132 pi-Stacking: D:Y.124, D:Y.124

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain A: R.37 Ligands: DTP.1, DTP.2 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Ligands: DTP.6, DTP.7 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: R.37 Ligands: DTP.9, DTP.10 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Ligands: DTP.14, DTP.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, R. et al., Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones. Structure (2016)

Release Date

2016-05-04

Peptides

Ribonucleoside-diphosphate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Ribonucleoside-diphosphate reductase