SMTL ID : 8vhn.1

Crystal Structure of E. coli class Ia ribonucleotide reductase alpha subunit bound to two ATP molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: V.7, K.9, R.10, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, I.58, H.59, K.91 Ligands: MG.2, ATP.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.9, A:R.10, A:R.16, A:N.18 Water bridges: A:R.10, A:H.59, A:K.91, A:K.91 Salt bridges: A:K.9, A:K.9, A:R.10, A:R.10, A:K.91, A:K.91, A:K.91 ATP.3: 12 residues within 4Å: Chain A: K.9, K.21, R.24, V.25, W.28, H.59, F.87, H.88, K.91, F.97 Ligands: ATP.1, MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.24 Water bridges: A:K.9, A:K.9, A:H.59, A:K.91, A:K.91 Salt bridges: A:K.9, A:K.9, A:K.21, A:K.21, A:K.91 pi-Stacking: A:W.28, A:W.28, A:W.28, A:F.87, A:F.97 ATP.4: 13 residues within 4Å: Chain A: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, T.276, F.281 Chain B: S.249, C.292 Ligands: MG.5 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.232, A:L.234, A:R.269, B:S.249 Water bridges: A:S.233, A:S.233, A:D.235, A:R.269, A:R.269, A:G.270, A:G.270, A:T.276 Salt bridges: A:R.262, A:R.269 ATP.8: 17 residues within 4Å: Chain B: V.7, K.9, R.10, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, I.58, H.59, I.62, K.91 Ligands: MG.9, ATP.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.9, B:R.10, B:E.15, B:E.15, B:N.18, B:T.55 Water bridges: B:K.21 Salt bridges: B:K.9, B:K.9, B:R.10, B:R.10, B:K.91, B:K.91 ATP.10: 12 residues within 4Å: Chain B: K.9, E.15, K.21, R.24, V.25, W.28, H.59, F.87, K.91, F.97 Ligands: ATP.8, MG.9 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:H.59 Water bridges: B:K.9, B:K.9, B:K.9, B:R.24, B:R.24, B:K.91 Salt bridges: B:K.9, B:K.9, B:K.21, B:K.21, B:R.24, B:R.24, B:K.91 pi-Stacking: B:W.28, B:W.28, B:W.28, B:F.87, B:F.97 ATP.11: 14 residues within 4Å: Chain A: S.249, C.292 Chain B: D.232, S.233, L.234, I.237, I.261, R.262, I.268, R.269, H.275, T.276, F.281 Ligands: MG.12 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.232, B:L.234, B:R.269, A:S.249 Water bridges: B:S.233, B:D.235, B:R.262, B:R.262, B:P.267, B:R.269, B:R.269, B:R.269, B:G.270, B:T.276 Salt bridges: B:R.262, B:R.269

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

MG.2: 2 residues within 4Å: Ligands: ATP.1, ATP.3 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Ligands: ATP.8, ATP.10 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: ATP.11 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: N.630, A.631, T.632, G.640, S.643, Q.654, V.655, V.656, P.657 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.630, A:S.643, A:Q.654, A:Q.654 Water bridges: A:N.633 GOL.13: 3 residues within 4Å: Chain B: D.598, E.600, A.601 No protein-ligand interaction detected (PLIP)

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 6 residues within 4Å: Chain A: G.32, H.34, D.76, Y.79, R.83, M.141 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.83 Salt bridges: A:D.76, A:R.83 MES.14: 8 residues within 4Å: Chain B: G.32, L.33, H.34, D.76, Y.79, R.83, M.141, T.142 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.83 Water bridges: B:Y.79, B:Y.79 Salt bridges: B:D.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Funk, M.A. et al., How ATP and dATP Act as Molecular Switches to Regulate Enzymatic Activity in the Prototypical Bacterial Class Ia Ribonucleotide Reductase. Biochemistry (2024)

Release Date

2024-09-04

Peptides

Ribonucleoside-diphosphate reductase 1 subunit alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase 1 subunit alpha

Related Entries With Identical Sequence