SMTL ID : 5cnt.1

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to UDP and dATP at 3.25 Angstroms resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-4-4-mer

Ligands

4 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 19 residues within 4Å: Chain A: P.208, T.209, S.224, C.225, A.252, 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 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.209, A:T.209, A:G.253, A:G.253, A:Q.294, A:Q.294, A:N.437, A:S.622, A:E.623, A:T.624, A:T.624, A:S.625 Water bridges: A:V.226, A:L.438 Salt bridges: A:R.298 pi-Cation interactions: A:R.298 UDP.7: 18 residues within 4Å: Chain B: 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 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.209, B:G.253, B:G.253, B:Q.294, B:R.298, B:N.437, B:S.622, B:E.623, B:T.624, B:S.625, B:S.625 Water bridges: B:V.226, B:L.438 Salt bridges: B:R.298 pi-Cation interactions: B:R.298 UDP.13: 18 residues within 4Å: Chain C: T.209, S.224, C.225, A.252, 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 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:T.209, C:T.209, C:G.253, C:G.253, C:Q.294, C:Q.294, C:R.298, C:N.437, C:S.622, C:E.623, C:T.624, C:T.624, C:T.624, C:S.625 Water bridges: C:S.224, C:L.438 Salt bridges: C:R.298 pi-Cation interactions: C:R.298 UDP.19: 19 residues within 4Å: Chain D: P.208, T.209, S.224, C.225, A.252, 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 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:T.209, D:G.253, D:G.253, D:Q.294, D:Q.294, D:R.298, D:N.437, D:S.622, D:E.623, D:T.624, D:S.625, D:S.625 Water bridges: D:V.226, D:L.438 Salt bridges: D:R.298 pi-Cation interactions: D:R.298

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

DTP.2: 17 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, F.87, K.91, G.95 Ligands: MG.3, DTP.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.25 Hydrogen bonds: A:R.10, A:E.15, A:N.18, A:H.59 Salt bridges: A:K.9, A:R.10, A:K.91, A:K.91, A:K.91 DTP.4: 8 residues within 4Å: Chain A: K.9, E.15, K.21, V.25, W.28, F.97 Ligands: DTP.2, MG.3 6 PLIP interactions: 6 interactions with chain A Salt bridges: A:K.9, A:K.9, A:K.21, A:K.21, A:K.91 pi-Stacking: A:F.97 DTP.5: 15 residues within 4Å: Chain A: D.232, S.233, L.234, I.237, I.261, R.262, I.268, R.269, H.275, T.276, F.281 Chain B: S.249, C.292, S.293 Ligands: MG.6 11 PLIP interactions: 9 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:R.262, A:R.262 Salt bridges: A:R.262 DTP.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, H.59, I.62, F.87, K.91 Ligands: MG.9, DTP.10 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.25 Hydrogen bonds: B:R.10, B:E.15, B:E.15, B:N.18, B:H.59, B:G.95 Water bridges: B:G.95 Salt bridges: B:K.9, B:R.10, B:K.91, B:K.91, B:K.91 DTP.10: 9 residues within 4Å: Chain B: K.9, K.21, R.24, V.25, W.28, F.87, F.97 Ligands: DTP.8, MG.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.28 Salt bridges: B:K.9, B:K.9, B:K.21, B:K.21, B:K.91 DTP.11: 15 residues within 4Å: Chain A: S.249, C.292, S.293 Chain B: D.232, S.233, L.234, I.261, R.262, I.268, R.269, F.274, H.275, T.276, F.281 Ligands: MG.12 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.234, B:F.281 Hydrogen bonds: B:D.232, B:L.234, B:R.269, B:R.269, B:T.276, A:S.293, A:S.293 Water bridges: B:R.262, B:R.262 Salt bridges: B:R.262 DTP.14: 17 residues within 4Å: Chain C: 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, F.87, K.91 Ligands: MG.15, DTP.16 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.25 Hydrogen bonds: C:R.10, C:E.15, C:N.18, C:T.55, C:H.59, C:G.95 Salt bridges: C:K.9, C:R.10, C:R.10, C:K.91, C:K.91, C:K.91 DTP.16: 9 residues within 4Å: Chain C: K.9, K.21, R.24, V.25, W.28, F.87, F.97 Ligands: DTP.14, MG.15 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.28 Salt bridges: C:K.9, C:K.9, C:K.21, C:K.21, C:K.91 pi-Stacking: C:F.97 DTP.17: 14 residues within 4Å: Chain C: D.232, S.233, L.234, I.261, R.262, I.268, R.269, H.275, T.276, F.281 Chain D: S.249, C.292, S.293 Ligands: MG.18 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.234, C:F.281 Hydrogen bonds: C:D.232, C:L.234, C:R.269, C:R.269, C:T.276, D:S.293, D:S.293 Water bridges: C:R.262, C:R.262 Salt bridges: C:R.262 DTP.20: 18 residues within 4Å: Chain D: 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, F.87, K.91, G.95 Ligands: MG.21, DTP.22 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:V.25 Hydrogen bonds: D:R.10, D:E.15, D:E.15, D:N.18, D:T.55, D:H.59 Salt bridges: D:K.9, D:K.9, D:K.9, D:R.10, D:K.91, D:K.91, D:K.91 DTP.22: 10 residues within 4Å: Chain D: K.9, E.15, K.21, R.24, V.25, W.28, K.91, F.97 Ligands: DTP.20, MG.21 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:W.28 Salt bridges: D:K.9, D:K.9, D:K.21, D:K.21, D:K.91 pi-Stacking: D:F.97 DTP.23: 15 residues within 4Å: Chain C: S.249, C.292, S.293 Chain D: D.232, S.233, L.234, I.261, R.262, I.268, R.269, F.274, H.275, T.276, F.281 Ligands: MG.24 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.234, D:F.281 Hydrogen bonds: D:D.232, D:L.234, D:R.269, D:T.276, C:S.293, C:S.293 Water bridges: D:R.262, D:R.262 Salt bridges: D:R.262, D:R.269

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

MG.3: 2 residues within 4Å: Ligands: DTP.2, DTP.4 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: DTP.5 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Ligands: DTP.8, DTP.10 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: DTP.11 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain C: K.91 Ligands: DTP.14, DTP.16 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: DTP.17 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Ligands: DTP.20, DTP.22 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Ligands: DTP.23 No protein-ligand interaction detected (PLIP)

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

FEO.25: 7 residues within 4Å: Chain E: D.84, E.115, H.118, E.204, F.208, E.238, H.241 8 PLIP interactions: 6 interactions with chain E, 2 Ligand-Water interactions, Metal complexes: E:D.84, E:E.115, E:E.115, E:H.118, E:E.204, E:H.241, H2O.2, H2O.2 FEO.26: 6 residues within 4Å: Chain F: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 6 interactions with chain F, 2 Ligand-Water interactions, Metal complexes: F:D.84, F:D.84, F:E.115, F:H.118, F:E.204, F:H.241, H2O.2, H2O.2 FEO.27: 6 residues within 4Å: Chain G: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 6 interactions with chain G, 2 Ligand-Water interactions, Metal complexes: G:D.84, G:E.115, G:E.115, G:H.118, G:E.204, G:H.241, H2O.2, H2O.2 FEO.28: 6 residues within 4Å: Chain H: D.84, E.115, H.118, E.204, E.238, H.241 9 PLIP interactions: 7 interactions with chain H, 2 Ligand-Water interactions, Metal complexes: H:D.84, H:D.84, H:E.115, H:H.118, H:E.204, H:E.238, H:H.241, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimanyi, C.M. et al., Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli. Elife (2016)

Release Date

2016-01-20

Peptides

Ribonucleoside-diphosphate reductase 1 subunit alpha: ABCD
Ribonucleoside-diphosphate reductase 1 subunit beta: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Ribonucleoside-diphosphate reductase 1 subunit alpha

Ribonucleoside-diphosphate reductase 1 subunit beta

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