SMTL ID : 6aui.1

Human ribonucleotide reductase large subunit (alpha) with dATP and CDP

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

DTP.1: 14 residues within 4Å: Chain A: V.23, K.25, R.26, E.31, R.32, V.33, M.34, K.37, R.41, T.73, L.76, D.77, K.108 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.26, A:R.32, A:M.34, A:K.37, A:D.77 Water bridges: A:K.25, A:K.25 Salt bridges: A:K.25, A:R.26, A:R.41, A:K.108 DTP.3: 14 residues within 4Å: Chain A: D.246, S.247, I.248, I.275, R.276, I.282, A.283, G.284 Chain B: K.263, Y.305, V.306, D.307, G.309 Ligands: MG.4 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.248 Hydrogen bonds: A:D.246, A:I.248, A:A.283, A:G.284, B:D.307, B:D.307 Water bridges: A:D.246, A:R.276 Salt bridges: A:R.276, A:R.276, B:K.263, B:K.263 DTP.6: 15 residues within 4Å: Chain B: V.23, K.25, R.26, E.31, R.32, V.33, M.34, K.37, I.38, R.41, T.73, L.76, D.77, K.108 Ligands: MG.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.38 Hydrogen bonds: B:R.26, B:E.31, B:R.32, B:M.34, B:T.73, B:D.77 Water bridges: B:K.25, B:K.25, B:K.25, B:K.37, B:K.37 Salt bridges: B:K.25, B:R.26, B:R.26, B:R.41, B:K.108 DTP.8: 13 residues within 4Å: Chain A: K.263, D.307, G.309 Chain B: D.246, S.247, I.248, I.251, I.275, R.276, I.282, A.283, G.284 Ligands: MG.9 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.248 Hydrogen bonds: B:D.246, B:I.248, B:A.283, B:G.284, A:D.307, A:D.307 Water bridges: B:D.246, B:R.276 Salt bridges: B:R.276, B:R.276, A:K.263, A:K.263 DTP.11: 15 residues within 4Å: Chain C: V.23, K.25, R.26, E.31, R.32, V.33, M.34, K.37, I.38, R.41, T.73, L.76, D.77, K.108 Ligands: MG.12 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:I.38 Hydrogen bonds: C:R.26, C:R.32, C:M.34, C:D.77 Water bridges: C:K.25, C:K.25, C:K.25, C:K.37, C:K.37 Salt bridges: C:K.25, C:R.26, C:R.41, C:K.108 DTP.13: 15 residues within 4Å: Chain C: D.246, S.247, I.248, I.251, I.275, R.276, I.282, A.283, G.284 Chain D: K.263, Y.305, V.306, D.307, G.309 Ligands: MG.14 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.248 Hydrogen bonds: C:D.246, C:I.248, C:A.283, C:G.284, D:D.307, D:D.307 Water bridges: C:R.276, C:R.276 Salt bridges: C:R.276, C:R.276, D:K.263, D:K.263 DTP.16: 15 residues within 4Å: Chain D: V.23, K.25, R.26, E.31, R.32, V.33, M.34, K.37, I.38, R.41, T.73, L.76, D.77, K.108 Ligands: MG.17 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.38 Hydrogen bonds: D:R.26, D:E.31, D:R.32, D:M.34, D:T.73, D:D.77 Water bridges: D:K.25, D:K.37, D:K.37, D:K.37 Salt bridges: D:K.25, D:R.26, D:R.26, D:R.41, D:K.108 DTP.18: 15 residues within 4Å: Chain C: K.263, Y.305, D.307, G.309 Chain D: D.246, S.247, I.248, I.251, I.275, R.276, Y.281, I.282, A.283, G.284 Ligands: MG.19 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.248 Hydrogen bonds: D:D.246, D:I.248, D:A.283, D:G.284, C:D.307, C:D.307 Water bridges: D:D.246, D:R.276 Salt bridges: D:R.276, D:R.276, C:K.263, C:K.263 DTP.21: 13 residues within 4Å: Chain E: V.23, K.25, R.26, E.31, R.32, V.33, M.34, R.41, T.73, L.76, D.77, K.108 Ligands: MG.22 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:R.26, E:D.27, E:R.32, E:M.34, E:D.77 Water bridges: E:K.25, E:K.25, E:K.37 Salt bridges: E:K.25, E:R.26, E:R.41, E:K.108 DTP.23: 14 residues within 4Å: Chain E: D.246, S.247, I.248, I.275, R.276, I.282, A.283, G.284 Chain F: K.263, Y.305, V.306, D.307, G.309 Ligands: MG.24 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:I.248 Hydrogen bonds: E:D.246, E:I.248, E:A.283, E:G.284, F:D.307, F:D.307 Water bridges: E:R.276, E:R.276 Salt bridges: E:R.276, E:R.276, F:K.263, F:K.263 DTP.26: 15 residues within 4Å: Chain F: V.23, K.25, R.26, R.32, V.33, M.34, K.37, I.38, R.41, L.67, T.73, L.76, D.77, K.108 Ligands: MG.27 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:I.38 Hydrogen bonds: F:R.26, F:E.31, F:R.32, F:M.34, F:T.73, F:D.77 Water bridges: F:K.25, F:K.25, F:K.37, F:K.37 Salt bridges: F:K.25, F:R.26, F:R.26, F:R.41, F:K.108 DTP.28: 15 residues within 4Å: Chain E: K.263, Y.305, D.307, G.309 Chain F: D.246, S.247, I.248, I.251, I.275, R.276, Y.281, I.282, A.283, G.284 Ligands: MG.29 12 PLIP interactions: 8 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:I.248 Hydrogen bonds: F:D.246, F:A.283, F:G.284, E:D.307, E:D.307 Water bridges: F:R.276, F:R.276 Salt bridges: F:R.276, F:R.276, E:K.263, E:K.263

12 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.4: 1 residues within 4Å: Ligands: DTP.3 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: K.37 Ligands: DTP.6 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: DTP.8 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain C: K.37 Ligands: DTP.11 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: DTP.13 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain D: K.37 Ligands: DTP.16 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Ligands: DTP.18 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Ligands: DTP.21 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Ligands: DTP.23 No protein-ligand interaction detected (PLIP) MG.27: 2 residues within 4Å: Chain F: K.37 Ligands: DTP.26 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Ligands: DTP.28 No protein-ligand interaction detected (PLIP)

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

CDP.5: 16 residues within 4Å: Chain A: S.222, S.237, C.238, G.266, G.267, Q.308, R.313, N.447, C.449, E.451, L.466, P.623, T.624, A.625, S.626, T.627 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Y.175, A:Y.175, A:S.222, A:S.222, A:S.237, A:Q.308, A:R.313, A:N.447, A:E.451, A:T.624, A:A.625, A:S.626, A:S.626, A:T.627, A:T.627 Salt bridges: A:R.313 pi-Cation interactions: A:R.313 CDP.10: 16 residues within 4Å: Chain B: S.222, S.237, C.238, G.266, G.267, Q.308, R.313, N.447, C.449, E.451, L.466, P.623, T.624, A.625, S.626, T.627 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Y.175, B:S.222, B:S.222, B:S.237, B:Q.308, B:R.313, B:N.447, B:E.451, B:T.624, B:A.625, B:S.626, B:S.626, B:T.627, B:T.627, B:T.627, B:T.627 Salt bridges: B:R.313 CDP.15: 16 residues within 4Å: Chain C: S.222, S.237, C.238, G.266, G.267, Q.308, R.313, N.447, C.449, E.451, L.466, P.623, T.624, A.625, S.626, T.627 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.175, C:S.222, C:S.222, C:S.237, C:Q.308, C:R.313, C:N.447, C:E.451, C:T.624, C:A.625, C:S.626, C:S.626, C:T.627, C:T.627 Salt bridges: C:R.313 pi-Cation interactions: C:R.313 CDP.20: 16 residues within 4Å: Chain D: S.222, S.237, C.238, G.266, G.267, Q.308, R.313, N.447, C.449, E.451, L.466, P.623, T.624, A.625, S.626, T.627 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:S.222, D:S.222, D:S.237, D:Q.308, D:N.447, D:E.451, D:T.624, D:A.625, D:S.626, D:S.626, D:T.627, D:T.627, D:T.627, D:T.627 Salt bridges: D:R.313 pi-Cation interactions: D:R.313 CDP.25: 16 residues within 4Å: Chain E: S.222, S.237, C.238, G.266, G.267, Q.308, R.313, N.447, C.449, E.451, L.466, P.623, T.624, A.625, S.626, T.627 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:Y.175, E:Y.175, E:S.222, E:S.222, E:S.237, E:Q.308, E:R.313, E:R.313, E:N.447, E:E.451, E:T.624, E:A.625, E:S.626, E:S.626, E:T.627, E:T.627 Salt bridges: E:R.313 pi-Cation interactions: E:R.313 CDP.30: 16 residues within 4Å: Chain F: S.222, S.237, C.238, G.266, G.267, Q.308, R.313, N.447, C.449, E.451, L.466, P.623, T.624, A.625, S.626, T.627 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:Y.175, F:S.222, F:S.222, F:S.237, F:Q.308, F:R.313, F:N.447, F:E.451, F:T.624, F:A.625, F:S.626, F:S.626, F:T.627, F:T.627, F:T.627, F:T.627 Salt bridges: F:R.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brignole, E.J. et al., 3.3- angstrom resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound. Elife (2018)

Release Date

2018-04-18

Peptides

Ribonucleoside-diphosphate reductase large subunit: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Ribonucleoside-diphosphate reductase large subunit

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