SMTL ID : 9db2.1

Class Ia ribonucleotide reductase with mechanism-based inhibitor N3CDP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

DTP.1: 14 residues within 4Å: Chain A: D.232, S.233, L.234, I.237, I.261, R.262, I.268, R.269, H.275, F.281 Chain B: S.249, C.292, S.293 Ligands: MG.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.234, A:F.281 Hydrogen bonds: A:D.232, A:L.234, A:R.269, A:R.269, B:S.293, B:S.293 Water bridges: A:D.235, A:R.262, A:R.262, A:G.270 Salt bridges: A:R.262, A:R.269 DTP.9: 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, F.274, H.275, T.276 Ligands: MG.10 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.234 Hydrogen bonds: B:D.232, B:S.233, B:L.234, B:R.269, A:S.249 Water bridges: B:D.235, B:R.262, B:P.267, B:R.269, B:G.270 Salt bridges: B:R.262, B:R.269

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

MG.2: 1 residues within 4Å: Ligands: DTP.1 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Ligands: ATP.3, ATP.4 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: DTP.9 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: K.91 Ligands: ATP.7, ATP.8 No protein-ligand interaction detected (PLIP)

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

ATP.3: 10 residues within 4Å: Chain A: K.9, K.21, R.24, V.25, W.28, H.59, F.87, F.97 Ligands: ATP.4, MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.24, A:H.59 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: 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, H.59, I.62, K.91 Ligands: ATP.3, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.9, A:R.10, A:R.16, A:N.18 Salt bridges: A:K.9, A:K.9, A:R.10, A:R.10, A:K.91 ATP.7: 10 residues within 4Å: Chain B: K.9, K.21, V.25, W.28, H.59, F.87, K.91, F.97 Ligands: ATP.8, MG.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.91 Water bridges: B:K.9, B:F.97 Salt bridges: B:K.9, B:K.9, B:K.21, B:K.21, B:K.91 pi-Stacking: B:W.28, B:F.87, B:F.97 ATP.8: 15 residues within 4Å: Chain B: 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: ATP.7, MG.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.9, B:R.10, B:R.16, B:N.18, B:K.21 Water bridges: B:K.91 Salt bridges: B:K.9, B:K.9, B:R.10, B:K.91, B:K.91

1 x UNL: UNKNOWN LIGAND

UNL.6: 5 residues within 4Å: Chain A: C.225, N.437, C.439, E.441, M.620 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.437, A:C.439, A:E.441

1 x 01: 4-amino-1-{(3xi)-3-C-amino-2-deoxy-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-beta-D-threo-pentofuranosyl}pyrimidin-2(1H)-one

01.12: 21 residues within 4Å: Chain B: Y.155, P.208, T.209, S.224, C.225, G.253, Q.294, R.298, N.437, L.438, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625 Chain C: Q.350, E.351 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.438, C:Q.350 Hydrogen bonds: B:Y.155, B:T.209, B:T.209, B:Q.294, B:N.437, B:C.439, B:S.622, B:E.623, B:T.624, B:S.625, C:E.351, C:E.351 Water bridges: B:R.298, B:R.298, B:R.298, B:R.298, B:L.438, B:S.625, B:S.625 Salt bridges: B:R.298 pi-Cation interactions: B:R.298

2 x FEO: MU-OXO-DIIRON(Non-covalent)

FEO.13: 6 residues within 4Å: Chain C: D.85, E.116, H.119, E.205, E.239, H.242 9 PLIP interactions: 8 interactions with chain C, 1 Ligand-Water interactions Hydrogen bonds: C:E.205 Metal complexes: C:D.85, C:D.85, C:E.116, C:E.116, C:H.119, C:E.239, C:H.242, H2O.18 FEO.14: 7 residues within 4Å: Chain D: D.85, E.116, H.119, E.205, F.209, E.239, H.242 8 PLIP interactions: 7 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.85, D:E.116, D:E.116, D:E.116, D:H.119, D:E.205, D:H.242, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Westmoreland, D.E. et al., 2.6- angstrom resolution cryo-EM structure of a class Ia ribonucleotide reductase trapped with mechanism-based inhibitor N 3 CDP. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-11-06

Peptides

Ribonucleoside-diphosphate reductase 1 subunit alpha: AB
Ribonucleoside-diphosphate reductase 1 subunit beta: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ribonucleoside-diphosphate reductase 1 subunit alpha

Ribonucleoside-diphosphate reductase 1 subunit beta

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