SMTL ID : 8vhp.2 (3 other biounits)

Crystal structure of E. coli class Ia ribonucleotide reductase alpha subunit W28A variant bound to CDP and two molecules of ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.265, Q.269, P.518 Chain B: R.288 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.269, B:R.288 Salt bridges: A:K.265 SO4.2: 2 residues within 4Å: Chain A: K.548, N.557 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.557 Water bridges: A:K.548 Salt bridges: A:K.548 SO4.3: 4 residues within 4Å: Chain A: H.137, D.141, N.202, R.239 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.141 Water bridges: A:H.137, A:N.202, A:R.239 Salt bridges: A:R.239 SO4.10: 4 residues within 4Å: Chain A: V.55, S.56, I.57, S.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.57, A:S.58, A:S.58 SO4.11: 5 residues within 4Å: Chain A: R.91, G.659, Y.660, V.661, L.687 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.660, A:V.661 Salt bridges: A:R.91 SO4.12: 4 residues within 4Å: Chain A: R.288 Chain B: K.265, Q.269, P.518 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.288, B:Q.269 Water bridges: B:K.265 Salt bridges: B:K.265 SO4.13: 1 residues within 4Å: Chain B: N.557 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.557 Water bridges: B:N.557, B:N.557, B:L.558 Salt bridges: B:K.548 SO4.14: 3 residues within 4Å: Chain B: H.137, D.141, R.239 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.137, B:N.202 Salt bridges: B:R.239 SO4.21: 5 residues within 4Å: Chain B: I.89, S.90, R.91, V.661 Ligands: SO4.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.91 SO4.22: 4 residues within 4Å: Chain B: Y.211, R.214, I.502, R.506 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.211 Salt bridges: B:R.214, B:R.506 SO4.23: 5 residues within 4Å: Chain B: R.91, G.659, Y.660, V.661 Ligands: SO4.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.660, B:V.661 Salt bridges: B:R.91 SO4.24: 5 residues within 4Å: Chain B: Q.97, Y.98, V.675, P.676, D.677 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.97, B:Y.98, B:V.675, B:D.677

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

ATP.4: 16 residues within 4Å: Chain A: V.26, K.28, R.29, E.34, R.35, I.36, N.37, K.40, I.41, V.44, T.74, I.77, H.78, K.110 Ligands: MG.5, ATP.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.29, A:E.34, A:R.35, A:N.37, A:T.74 Water bridges: A:D.30, A:D.30 Salt bridges: A:K.28, A:K.28, A:R.29, A:K.110, A:K.110, A:K.110 ATP.6: 11 residues within 4Å: Chain A: K.28, E.34, K.40, V.44, H.78, F.106, H.107, K.110, F.116 Ligands: ATP.4, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.78, A:F.106 Salt bridges: A:K.28, A:K.28, A:K.40, A:K.40, A:K.110 pi-Stacking: A:F.106, A:F.116 ATP.7: 16 residues within 4Å: Chain A: D.251, S.252, L.253, I.256, I.280, R.281, I.287, R.288, H.294, T.295, F.300 Chain B: S.268, S.310, C.311, S.312 Ligands: MG.8 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:S.312, B:S.312, A:D.251, A:L.253, A:R.288 Water bridges: B:K.265, A:R.281, A:R.281, A:R.288 Salt bridges: A:R.281, A:R.288 ATP.15: 17 residues within 4Å: Chain B: V.26, K.28, R.29, E.34, R.35, I.36, N.37, K.40, I.41, V.44, T.74, H.78, I.81, K.110, G.114 Ligands: MG.16, ATP.17 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.29, B:R.35, B:N.37, B:T.74 Water bridges: B:R.29, B:R.29 Salt bridges: B:K.28, B:K.28, B:R.29, B:K.110, B:K.110, B:K.110 ATP.17: 11 residues within 4Å: Chain B: K.28, E.34, K.40, V.44, H.78, F.106, H.107, K.110, F.116 Ligands: ATP.15, MG.16 9 PLIP interactions: 9 interactions with chain B Water bridges: B:H.78 Salt bridges: B:K.28, B:K.28, B:K.40, B:K.40, B:K.110 pi-Stacking: B:F.106, B:F.116, B:F.116 ATP.18: 16 residues within 4Å: Chain A: S.268, S.310, C.311, S.312 Chain B: D.251, S.252, L.253, I.256, I.280, R.281, I.287, R.288, H.294, T.295, F.300 Ligands: MG.19 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.251, B:L.253, B:R.288, A:S.312, A:S.312 Water bridges: B:D.254, B:D.254, B:R.281 Salt bridges: B:R.281, B:R.288

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

MG.5: 2 residues within 4Å: Ligands: ATP.4, ATP.6 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: R.281 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Ligands: ATP.15, ATP.17 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain B: D.251 Ligands: ATP.18 No protein-ligand interaction detected (PLIP)

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.9: 18 residues within 4Å: Chain A: P.227, T.228, S.243, C.244, G.272, Q.313, R.317, N.456, L.457, C.458, E.460, L.483, M.639, P.640, S.641, E.642, T.643, S.644 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.228, A:T.228, A:Q.313, A:R.317, A:N.456, A:E.460, A:S.641, A:E.642, A:T.643, A:S.644, A:S.644, A:S.644 Water bridges: A:S.243, A:S.243, A:G.272, A:G.272, A:Q.313, A:R.317, A:R.317, A:L.457 Salt bridges: A:R.317 pi-Cation interactions: A:R.317 CDP.20: 18 residues within 4Å: Chain B: P.227, T.228, S.243, C.244, G.272, Q.313, R.317, N.456, L.457, C.458, E.460, L.483, M.639, P.640, S.641, E.642, T.643, S.644 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:T.228, B:T.228, B:T.228, B:T.228, B:G.272, B:Q.313, B:N.456, B:C.458, B:E.460, B:S.641, B:E.642, B:T.643, B:S.644, B:S.644 Water bridges: B:S.243, B:G.272, B:Q.313, B:R.317, B:R.317, B:R.317, B:R.317, B:L.457, B:T.643 Salt bridges: B:R.317 pi-Cation interactions: B:R.317

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
C

B
D

Ribonucleoside-diphosphate reductase 1 subunit alpha

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