SMTL ID : 5cnu.1

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to ADP and dGTP at 3.40 Angstroms resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-4-4-mer

Ligands

4 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 16 residues within 4Å: Chain A: D.232, S.233, L.234, I.237, I.261, R.262, I.268, R.269, F.274, H.275, T.276, F.281 Chain B: S.249, C.292, Q.294 Ligands: MG.2 13 PLIP interactions: 11 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, A:T.276, B:Q.294, B:Q.294 Water bridges: A:R.262, A:R.262 Salt bridges: A:R.262 pi-Cation interactions: A:H.275 DGT.9: 17 residues within 4Å: Chain A: S.249, S.291, C.292, Q.294 Chain B: D.232, S.233, L.234, I.237, I.261, R.262, I.268, R.269, F.274, H.275, T.276, F.281 Ligands: MG.10 15 PLIP interactions: 13 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:Q.294, A:Q.294 Water bridges: B:R.262, B:R.262, B:T.276, B:G.277, B:G.277 Salt bridges: B:R.262 DGT.14: 16 residues within 4Å: Chain C: D.232, S.233, L.234, I.237, I.261, R.262, I.268, R.269, H.275, T.276, F.281 Chain D: S.249, S.291, C.292, Q.294 Ligands: MG.15 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.234, C:F.281 Hydrogen bonds: C:D.232, C:D.232, C:L.234, C:R.269, C:R.269, C:T.276, D:Q.294, D:Q.294 Water bridges: C:R.262, C:R.262 Salt bridges: C:R.262, C:R.262 pi-Cation interactions: C:H.275 DGT.19: 16 residues within 4Å: Chain C: S.249, S.291, C.292, Q.294 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.20 14 PLIP interactions: 12 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:P.267, D:R.269, D:R.269, D:T.276, C:Q.294, C:Q.294 Water bridges: D:R.262, D:R.262 Salt bridges: D:R.262 pi-Cation interactions: D:H.275

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

MG.2: 1 residues within 4Å: Ligands: DGT.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DAT.4 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: DAT.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: DGT.9 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: DAT.12 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: DGT.14 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Ligands: DAT.17 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: DGT.19 No protein-ligand interaction detected (PLIP)

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 21 residues within 4Å: Chain A: P.208, T.209, S.224, C.225, A.252, G.253, R.298, G.299, G.300, A.301, N.437, L.438, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.209, A:T.209, A:T.209, A:R.298, A:G.299, A:A.301, A:N.437, A:C.439, A:E.441, A:S.622, A:E.623, A:T.624, A:T.624, A:S.625, A:S.625 Water bridges: A:L.438, A:L.438 Salt bridges: A:R.298 pi-Cation interactions: A:R.298, A:R.298 ADP.6: 20 residues within 4Å: Chain B: P.208, T.209, S.224, C.225, A.252, G.253, R.298, G.299, G.300, A.301, N.437, 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 B Hydrogen bonds: B:T.209, B:T.209, B:T.209, B:S.224, B:R.298, B:G.299, B:A.301, B:N.437, B:E.441, B:S.622, B:E.623, B:T.624, B:S.625 Water bridges: B:S.224, B:L.438 Salt bridges: B:R.298 pi-Cation interactions: B:R.298, B:R.298 ADP.11: 20 residues within 4Å: Chain C: P.208, T.209, S.224, C.225, A.252, G.253, R.298, G.299, G.300, A.301, N.437, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:T.209, C:T.209, C:T.209, C:T.209, C:R.298, C:G.299, C:A.301, C:N.437, C:C.439, C:E.441, C:S.622, C:E.623, C:T.624, C:T.624, C:S.625 Water bridges: C:L.438 Salt bridges: C:R.298 pi-Cation interactions: C:R.298, C:R.298 ADP.16: 20 residues within 4Å: Chain D: P.208, T.209, S.224, C.225, A.252, G.253, R.298, G.299, G.300, A.301, N.437, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:T.209, D:T.209, D:R.298, D:G.299, D:A.301, D:N.437, D:E.441, D:S.622, D:E.623, D:T.624, D:S.625, 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

4 x DAT: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE(Non-covalent)

DAT.4: 15 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 Ligands: MG.5 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 Water bridges: A:K.9, A:K.91 Salt bridges: A:K.9, A:R.10, A:K.91 DAT.7: 16 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.8 10 PLIP interactions: 10 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 Water bridges: B:K.9 Salt bridges: B:K.9, B:R.10, B:K.91 DAT.12: 15 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, F.87, K.91 Ligands: MG.13 11 PLIP interactions: 11 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 Water bridges: C:K.9 Salt bridges: C:K.9, C:R.10, C:K.91, C:K.91 DAT.17: 17 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, I.58, H.59, I.62, F.87, K.91 Ligands: MG.18 13 PLIP interactions: 13 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 Water bridges: D:K.9, D:K.91 Salt bridges: D:K.9, D:R.10, D:K.91, D:K.91

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

FEO.21: 6 residues within 4Å: Chain E: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 8 interactions with chain E, Metal complexes: E:D.84, E:D.84, E:E.115, E:E.115, E:E.115, E:H.118, E:E.204, E:E.238 FEO.22: 6 residues within 4Å: Chain F: D.84, E.115, H.118, E.204, E.238, H.241 9 PLIP interactions: 7 interactions with chain F, 2 Ligand-Water interactions, Water bridges: F:Q.87 Metal complexes: F:D.84, F:D.84, F:E.115, F:H.118, F:E.204, F:H.241, H2O.3, H2O.4 FEO.23: 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.4, H2O.4 FEO.24: 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, Water bridges: H:Q.87 Metal complexes: H:D.84, H:D.84, H:E.115, H:H.118, H:E.204, H:H.241, H2O.4, H2O.4

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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