SMTL ID : 8p28.1

Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

DTP.1: 14 residues within 4Å: Chain A: R.196, P.197, K.199, R.200, T.203, V.206, L.207, I.210 Chain B: Q.294, E.297, A.298, H.301, N.302 Ligands: MG.8 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:Q.294, B:E.297, A:R.196, A:R.196, A:K.199, A:R.200, A:R.200 Salt bridges: A:R.196, A:K.199, A:K.199, A:K.199, A:R.200 DTP.2: 13 residues within 4Å: Chain A: V.9, K.11, R.12, G.18, F.19, N.20, K.23, I.24, A.27, V.61, I.64, Q.65 Ligands: DTP.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.64 Hydrogen bonds: A:G.18, A:N.20, A:Q.65 Salt bridges: A:K.11, A:K.11, A:R.12, A:R.12 pi-Stacking: A:F.19 DTP.3: 13 residues within 4Å: Chain A: R.12, A.27, K.30, A.31, H.34, Q.65, K.83, Y.84, Y.87, R.88, R.91, R.95 Ligands: DTP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.87 Hydrogen bonds: A:H.34, A:Q.65, A:Y.87, A:Y.87 Salt bridges: A:R.12, A:R.12, A:K.30, A:R.91, A:R.95 pi-Stacking: A:Y.87, A:Y.87 DTP.5: 13 residues within 4Å: Chain A: E.297, A.298, H.301, N.302 Chain B: S.195, R.196, P.197, A.198, K.199, R.200, T.203, V.206 Ligands: MG.4 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:Q.294, A:N.302, B:S.195, B:R.196, B:R.196, B:K.199 Salt bridges: B:R.196, B:K.199, B:R.200 DTP.6: 12 residues within 4Å: Chain B: K.11, R.12, G.18, N.20, K.23, I.24, V.61, I.64, Q.65, I.68, Y.84 Ligands: DTP.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.24, B:I.64 Hydrogen bonds: B:G.18, B:N.20, B:Y.84, B:Y.84 Salt bridges: B:K.11, B:R.12 pi-Stacking: B:F.19 DTP.7: 9 residues within 4Å: Chain B: R.12, A.27, A.31, Q.65, K.83, Y.84, Y.87, R.95 Ligands: DTP.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.84, B:Y.87 Hydrogen bonds: B:R.12, B:Q.65 Salt bridges: B:R.12, B:K.30, B:R.91, B:R.95 pi-Stacking: B:Y.87, B:Y.87 DTP.9: 14 residues within 4Å: Chain C: S.195, R.196, P.197, K.199, R.200, T.203, V.206, L.207, I.210 Chain D: Q.294, A.298, H.301, N.302 Ligands: MG.12 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.196, C:R.196, C:K.199, C:T.203, D:H.301 Salt bridges: C:R.196, C:R.200, C:R.200 DTP.10: 13 residues within 4Å: Chain C: V.9, K.11, R.12, G.18, F.19, N.20, K.23, I.24, V.61, I.64, Q.65, Y.84 Ligands: DTP.11 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.18, C:N.20, C:Q.65, C:Y.84 Salt bridges: C:K.11, C:K.11, C:R.12 DTP.11: 12 residues within 4Å: Chain C: R.12, A.27, K.30, A.31, H.34, Q.65, K.83, Y.84, Y.87, R.91, R.95 Ligands: DTP.10 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.87 Hydrogen bonds: C:K.30, C:H.34, C:H.34, C:Q.65, C:Q.65, C:Y.87 Salt bridges: C:R.12, C:R.12, C:K.30, C:R.91, C:R.95 pi-Stacking: C:Y.87, C:Y.87 DTP.14: 13 residues within 4Å: Chain C: E.297, A.298, H.301, N.302 Chain D: S.195, R.196, P.197, A.198, K.199, R.200, T.203, V.206 Ligands: MG.13 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:Q.294, C:N.302, D:S.195, D:R.196, D:R.196, D:K.199, D:T.203 Salt bridges: D:R.196, D:K.199, D:R.200 DTP.15: 9 residues within 4Å: Chain D: R.12, N.20, K.23, I.24, V.61, I.64, Q.65, I.68 Ligands: DTP.16 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:I.24, D:I.64 Hydrogen bonds: D:N.20, D:Y.84, D:Y.84 Salt bridges: D:R.12 DTP.16: 12 residues within 4Å: Chain C: E.149 Chain D: R.12, A.27, A.31, H.34, Q.65, K.83, Y.84, Y.87, R.91, R.95 Ligands: DTP.15 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.84, D:Y.87 Hydrogen bonds: D:Q.65, C:E.149 Salt bridges: D:R.12, D:K.30, D:R.91, D:R.95 pi-Stacking: D:Y.87, D:Y.87

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: Q.294, E.297 Ligands: DTP.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.297 MG.8: 4 residues within 4Å: Chain A: R.200 Chain B: Q.294, E.297 Ligands: DTP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.297 MG.12: 3 residues within 4Å: Chain C: R.200 Chain D: Q.294 Ligands: DTP.9 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain C: Q.294, E.297 Ligands: DTP.14 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bimai, O. et al., Activity modulation in anaerobic ribonucleotide reductase: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site. To Be Published

Release Date

2023-08-30

Peptides

Anaerobic ribonucleoside-triphosphate reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Anaerobic ribonucleoside-triphosphate reductase

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