SMTL ID : 8vhp.4 (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

8 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.269 Water bridges: A:Q.269 Salt bridges: A:K.265, B:R.288 SO4.2: 2 residues within 4Å: Chain A: K.548, N.557 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.557 Water bridges: A:N.557, A:N.557 Salt bridges: A:K.548 SO4.9: 3 residues within 4Å: Chain A: 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 SO4.10: 1 residues within 4Å: Chain B: N.557 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.557 Water bridges: B:N.557 Salt bridges: B:K.548 SO4.11: 3 residues within 4Å: Chain B: H.137, D.141, R.239 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.141 Water bridges: B:N.202, B:N.202 Salt bridges: B:R.239 SO4.18: 4 residues within 4Å: Chain B: V.55, S.56, I.57, S.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.56, B:I.57, B:S.58 SO4.19: 3 residues within 4Å: Chain B: I.89, S.90, R.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.89, B:R.91 Salt bridges: B:R.91 SO4.20: 3 residues within 4Å: Chain B: P.204, R.205, E.206 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.205

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

ATP.3: 17 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, I.81, K.110 Ligands: MG.4, ATP.5 14 PLIP interactions: 14 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, A:K.40 Salt bridges: A:K.28, A:K.28, A:R.29, A:K.110, A:K.110, A:K.110 ATP.5: 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.3, MG.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.78 Water bridges: A:K.110, A:F.116 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, A:F.116 ATP.6: 14 residues within 4Å: Chain A: D.251, S.252, L.253, I.256, R.281, I.287, R.288, H.294, T.295, F.300 Chain B: S.268, C.311, S.312 Ligands: MG.7 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.251, A:L.253, A:R.288, B:S.312, B:S.312 Water bridges: A:D.254, A:R.281, A:R.281, A:R.288, A:G.289, A:G.289 Salt bridges: A:R.281, A:R.288 ATP.12: 15 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, K.110 Ligands: MG.13, ATP.14 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.29, B:R.35, B:N.37, B:T.74 Water bridges: B:K.28, B:K.28, B:D.30, B:D.30, B:H.78, B:H.78 Salt bridges: B:K.28, B:K.28, B:R.29, B:R.29, B:K.110, B:K.110, B:K.110 ATP.14: 9 residues within 4Å: Chain B: K.28, K.40, V.44, H.78, F.106, K.110, F.116 Ligands: ATP.12, MG.13 11 PLIP interactions: 11 interactions with chain B Water bridges: B:K.28, B:K.28, B:R.43, 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 ATP.15: 15 residues within 4Å: Chain A: S.268, 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.16 8 PLIP interactions: 6 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 Salt bridges: B:R.281, B:R.288

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

MG.4: 2 residues within 4Å: Ligands: ATP.3, ATP.5 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Ligands: ATP.12, ATP.14 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: ATP.15 No protein-ligand interaction detected (PLIP)

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

CDP.8: 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 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:T.228, A:T.228, A:T.228, A:G.272, A:Q.313, A:R.317, A:N.456, A:C.458, 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:V.245, A:Q.313, A:R.317, A:R.317, A:R.317, A:L.457, A:T.643 Salt bridges: A:R.317 pi-Cation interactions: A:R.317 CDP.17: 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 23 PLIP interactions: 23 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: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: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

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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
G

B
H

Ribonucleoside-diphosphate reductase 1 subunit alpha

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