- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.95 Å
- Oligo State
- hetero-4-4-mer
- Ligands
- 8 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)
DTP.1: 16 residues within 4Å:- Chain A: V.7, K.9, R.10, D.11, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, H.59, I.62, F.87, K.91
14 PLIP interactions:14 interactions with chain A- Hydrophobic interactions: A:K.21, A:V.25
- Hydrogen bonds: A:R.10, A:E.15, A:N.18, A:T.55, A:H.59
- Salt bridges: A:K.9, A:K.9, A:R.10, A:K.21, A:K.91, A:K.91, A:K.91
DTP.3: 14 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
- Ligands: MG.4
10 PLIP interactions:9 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:L.234, A:F.281
- Hydrogen bonds: A:D.232, A:L.234, A:R.269, A:H.275, A:T.276, B:S.249
- Salt bridges: A:R.262, A:R.269
DTP.5: 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, I.58, H.59, I.62, F.87, K.91
14 PLIP interactions:14 interactions with chain B- Hydrophobic interactions: B:V.25
- Hydrogen bonds: B:R.10, B:R.10, B:D.11, B:E.15, B:E.15, B:N.18, B:T.55, B:H.59
- Salt bridges: B:K.9, B:K.9, B:R.10, B:K.91, B:K.91
DTP.7: 12 residues within 4Å:- Chain A: S.249, C.292
- Chain B: D.232, S.233, L.234, R.262, I.268, R.269, F.274, H.275, T.276
- Ligands: MG.8
9 PLIP interactions:8 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:L.234
- Hydrogen bonds: B:D.232, B:L.234, B:R.269, B:H.275, B:T.276, A:S.249
- Salt bridges: B:R.262, B:R.269
DTP.9: 14 residues within 4Å:- Chain C: 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
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:V.25
- Hydrogen bonds: C:K.9, C:R.10, C:E.15, C:N.18, C:T.55, C:H.59
- Salt bridges: C:K.9, C:K.9, C:R.10, C:R.10, C:K.91
DTP.11: 12 residues within 4Å:- Chain C: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, T.276
- Chain D: S.249, C.292
- Ligands: MG.12
9 PLIP interactions:8 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:L.234
- Hydrogen bonds: C:D.232, C:L.234, C:R.269, C:H.275, C:T.276, D:S.249
- Salt bridges: C:R.262, C:R.269
DTP.13: 14 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
13 PLIP interactions:13 interactions with chain D- Hydrophobic interactions: D:V.25
- Hydrogen bonds: D:K.9, 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:R.10, D:H.59, D:K.91
DTP.15: 14 residues within 4Å:- Chain C: S.249, C.292
- Chain D: D.232, S.233, L.234, I.237, I.261, R.262, I.268, R.269, H.275, T.276, F.281
- Ligands: MG.16
9 PLIP interactions:8 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:L.234, D:I.237
- Hydrogen bonds: D:D.232, D:L.234, D:R.269, D:T.276, C:S.249
- Salt bridges: D:R.262, D:R.269
- 4 x DAT: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE(Non-covalent)
DAT.2: 14 residues within 4Å:- Chain A: P.208, T.209, C.225, R.251, N.437, L.438, C.439, E.441, L.464, P.621, S.622, E.623, T.624, S.625
10 PLIP interactions:10 interactions with chain A- Hydrogen bonds: A:T.209, A:T.209, A:N.437, A:E.441, A:T.624, A:T.624, A:T.624, A:S.625, A:S.625, A:S.625
DAT.6: 17 residues within 4Å:- Chain B: P.208, T.209, S.224, C.225, R.251, A.252, G.253, N.437, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:T.209, B:T.209, B:N.437, B:E.441, B:T.624, B:T.624, B:T.624, B:S.625, B:S.625
DAT.10: 16 residues within 4Å:- Chain C: P.208, T.209, S.224, C.225, R.251, N.437, L.438, C.439, E.441, L.464, M.620, P.621, S.622, E.623, T.624, S.625
11 PLIP interactions:11 interactions with chain C- Hydrogen bonds: C:T.209, C:T.209, C:T.209, C:N.437, C:E.441, C:E.623, C:T.624, C:T.624, C:T.624, C:S.625, C:S.625
DAT.14: 13 residues within 4Å:- Chain D: Y.155, P.208, T.209, C.225, N.437, L.438, C.439, L.464, P.621, S.622, E.623, T.624, S.625
11 PLIP interactions:11 interactions with chain D- Hydrogen bonds: D:Y.155, D:T.209, D:N.437, D:S.622, D:E.623, D:T.624, D:T.624, D:T.624, D:T.624, D:S.625, D:S.625
- 4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.4: 1 residues within 4Å:- Ligands: DTP.3
No protein-ligand interaction detected (PLIP)MG.8: 1 residues within 4Å:- Ligands: DTP.7
No protein-ligand interaction detected (PLIP)MG.12: 1 residues within 4Å:- Ligands: DTP.11
No protein-ligand interaction detected (PLIP)MG.16: 2 residues within 4Å:- Chain D: D.232
- Ligands: DTP.15
No protein-ligand interaction detected (PLIP)- 4 x FEO: MU-OXO-DIIRON(Non-covalent)
FEO.17: 7 residues within 4Å:- Chain E: D.84, E.115, H.118, E.204, F.208, E.238, H.241
9 PLIP interactions:7 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:E.238, E:H.241, H2O.1, H2O.1
FEO.18: 7 residues within 4Å:- Chain F: D.84, E.115, H.118, E.204, F.208, E.238, H.241
8 PLIP interactions:6 interactions with chain F, 2 Ligand-Water interactions,- Metal complexes: F:D.84, F:E.115, F:E.115, F:H.118, F:E.204, F:H.241, H2O.1, H2O.1
FEO.19: 7 residues within 4Å:- Chain G: D.84, E.115, H.118, E.204, F.208, 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.1, H2O.1
FEO.20: 7 residues within 4Å:- Chain H: D.84, E.115, H.118, E.204, F.208, E.238, H.241
8 PLIP interactions:6 interactions with chain H, 2 Ligand-Water interactions,- Metal complexes: H:D.84, H:E.115, H:E.115, H:H.118, H:E.204, H:H.241, H2O.1, H2O.1
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zimanyi, C.M. et al., Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase. Structure (2012)
- Release Date
- 2012-07-04
- Peptides
- Ribonucleoside-diphosphate reductase 1 subunit alpha: ABCD
Ribonucleoside-diphosphate reductase 1 subunit beta: EFGH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
H
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.95 Å
- Oligo State
- hetero-4-4-mer
- Ligands
- 8 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)
- 4 x DAT: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 4 x FEO: MU-OXO-DIIRON(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zimanyi, C.M. et al., Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase. Structure (2012)
- Release Date
- 2012-07-04
- Peptides
- Ribonucleoside-diphosphate reductase 1 subunit alpha: ABCD
Ribonucleoside-diphosphate reductase 1 subunit beta: EFGH - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
H