SMTL ID : 7agj.1

Ribonucleotide Reductase R1 protein from Aquifex aeolicus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: V.5, K.7, R.8, E.13, K.14, L.15, D.16, K.19, I.20, A.23, T.52, Q.56, K.88, H.92 Ligands: ATP.2, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.7, A:R.8, A:K.14, A:D.16, A:K.19, A:Q.56 Salt bridges: A:K.7, A:K.88, A:K.88 ATP.2: 11 residues within 4Å: Chain A: K.7, E.13, K.19, F.26, Y.84, K.88, R.99, Y.105 Ligands: ATP.1, MG.5, SO4.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.105 Salt bridges: A:K.7, A:K.7, A:K.19, A:K.19, A:K.88 pi-Stacking: A:F.26, A:Y.84, A:Y.105, A:Y.105 ATP.13: 16 residues within 4Å: Chain B: V.5, K.7, R.8, E.13, K.14, L.15, D.16, K.19, I.20, A.23, T.52, Q.56, L.59, K.88 Ligands: ATP.14, MG.16 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.7, B:R.8, B:K.14, B:D.16, B:K.19, B:T.52, B:Q.56 Salt bridges: B:K.7, B:R.8, B:K.88, B:K.88 ATP.14: 9 residues within 4Å: Chain B: K.7, K.19, F.26, Y.84, K.88, R.99, Y.105 Ligands: ATP.13, MG.16 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.99, B:Y.105 Salt bridges: B:K.7, B:K.7, B:K.19, B:K.19, B:K.88 pi-Stacking: B:F.26, B:Y.84, B:Y.105, B:Y.105

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: D.73, Y.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.73

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 2 residues within 4Å: Chain A: T.476, G.477 No protein-ligand interaction detected (PLIP) PEG.15: 3 residues within 4Å: Chain B: D.73, Y.76, L.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.717

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: K.88 Ligands: ATP.1, ATP.2 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain B: K.88 Ligands: ATP.13, ATP.14 No protein-ligand interaction detected (PLIP)

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

SO4.6: 4 residues within 4Å: Chain A: A.699, R.700, F.701, T.727 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.700, A:F.701, A:F.701 Salt bridges: A:R.700 SO4.7: 5 residues within 4Å: Chain A: K.88, S.97, L.98, R.99 Ligands: ATP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.98, A:R.99 Salt bridges: A:K.88 SO4.8: 3 residues within 4Å: Chain A: T.219, G.682, S.683 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.219, A:S.683 Water bridges: A:T.219, A:T.219 SO4.9: 3 residues within 4Å: Chain A: G.418, E.419, R.469 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.419 Salt bridges: A:R.469 SO4.10: 2 residues within 4Å: Chain A: W.370, Y.435 No protein-ligand interaction detected (PLIP) SO4.11: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.726 SO4.12: 4 residues within 4Å: Chain A: S.641, V.642, E.643, R.659 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.641, A:V.642, A:E.643 Salt bridges: A:R.659 SO4.17: 4 residues within 4Å: Chain B: K.88, S.97, L.98, R.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.98, B:R.99 Salt bridges: B:K.88 SO4.18: 5 residues within 4Å: Chain B: K.106, Y.108, N.109, R.110, K.111 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.109, B:R.110, B:K.111 Salt bridges: B:K.106 SO4.19: 4 residues within 4Å: Chain B: S.641, V.642, E.643, R.659 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.642, B:E.643 Salt bridges: B:R.659 SO4.20: 4 residues within 4Å: Chain B: A.699, R.700, F.701, Y.722 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.700, B:F.701 Salt bridges: B:R.700

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rehling, D. et al., Structural and Biochemical Investigation of Class I Ribonucleotide Reductase from the Hyperthermophile Aquifex aeolicus. Biochemistry (2022)

Release Date

2021-10-06

Peptides

Ribonucleoside-diphosphate reductase subunit alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase subunit alpha