SMTL ID : 3uus.1

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 5.65 Å

Oligo State

hetero-4-4-mer

Ligands

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

DTP.1: 12 residues within 4Å: Chain A: V.7, K.9, E.15, R.16, I.17, N.18, I.22, T.55, I.58, H.59, F.87, K.91 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.22 Hydrogen bonds: A:K.9, A:E.15, A:N.18, A:T.55 Salt bridges: A:K.9, A:K.9, A:H.59, A:K.91, A:K.91 DTP.2: 12 residues within 4Å: Chain A: D.232, S.233, L.234, I.237, I.261, R.262, I.268, H.275, T.276, F.281 Chain B: S.249, C.292 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.234, A:F.281 Hydrogen bonds: A:D.232, A:D.232, A:L.234, A:R.269, A:H.275, A:T.276 Salt bridges: A:R.262, A:R.262 DTP.3: 14 residues within 4Å: Chain B: V.7, K.9, R.10, E.15, R.16, N.18, K.21, I.22, V.25, T.55, I.58, H.59, F.87, K.91 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.22 Hydrogen bonds: B:K.9, B:R.10, B:E.15, B:E.15, B:N.18, B:I.22, B:T.55, B:H.59 Salt bridges: B:K.9, B:K.9, B:H.59, B:K.91, B:K.91, B:K.91 DTP.4: 13 residues within 4Å: Chain A: S.249, C.292 Chain B: D.232, S.233, L.234, I.237, R.262, I.268, R.269, F.274, H.275, T.276, F.281 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.234, B:I.237, B:F.281 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 DTP.5: 12 residues within 4Å: Chain C: V.7, E.15, R.16, I.17, N.18, K.21, I.22, T.55, I.58, H.59, F.87, K.91 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.22 Hydrogen bonds: C:E.15, C:N.18, C:I.22, C:T.55 Salt bridges: C:K.9, C:K.9, C:H.59, C:K.91, C:K.91, C:K.91 DTP.6: 14 residues within 4Å: Chain C: D.232, S.233, L.234, I.237, I.261, R.262, P.267, I.268, R.269, H.275, T.276, F.281 Chain D: S.249, C.292 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.281 Hydrogen bonds: C:L.234, C:P.267, C:R.269, C:H.275, C:T.276 Salt bridges: C:R.262 DTP.7: 14 residues within 4Å: Chain D: V.7, K.9, E.15, R.16, I.17, N.18, K.21, I.22, V.25, T.55, H.59, F.87, K.91, G.95 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:R.16, D:N.18, D:N.18, D:T.55 Salt bridges: D:K.9, D:K.9, D:H.59, D:K.91, D:K.91, D:K.91 pi-Cation interactions: D:K.21 DTP.8: 14 residues within 4Å: Chain C: S.249, C.292 Chain D: D.232, S.233, L.234, I.237, I.261, R.262, P.267, I.268, R.269, H.275, T.276, F.281 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.237, D:F.281 Hydrogen bonds: D:D.232, D:D.232, D:L.234, D:R.269, D:T.276, C:S.249 Salt bridges: D:R.262

8 x FE: FE (III) ION(Non-covalent)

FE.9: 5 residues within 4Å: Chain E: D.84, E.115, H.118, E.238 Ligands: FE.10 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.84, E:D.84, E:E.115, E:H.118 FE.10: 6 residues within 4Å: Chain E: W.111, E.115, E.204, E.238, H.241 Ligands: FE.9 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.115, E:E.204, E:E.238, E:E.238, E:H.241 FE.11: 5 residues within 4Å: Chain F: D.84, E.115, H.118, E.238 Ligands: FE.12 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.84, F:D.84, F:E.115, F:H.118 FE.12: 6 residues within 4Å: Chain F: W.111, E.115, E.204, E.238, H.241 Ligands: FE.11 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:E.115, F:E.204, F:E.238, F:E.238, F:H.241 FE.13: 5 residues within 4Å: Chain G: D.84, E.115, H.118, E.238 Ligands: FE.14 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.84, G:D.84, G:E.115, G:H.118 FE.14: 6 residues within 4Å: Chain G: W.111, E.115, E.204, E.238, H.241 Ligands: FE.13 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.115, G:E.204, G:E.238, G:E.238, G:H.241 FE.15: 5 residues within 4Å: Chain H: D.84, E.115, H.118, E.238 Ligands: FE.16 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.84, H:D.84, H:E.115, H:H.118 FE.16: 6 residues within 4Å: Chain H: W.111, E.115, E.204, E.238, H.241 Ligands: FE.15 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.115, H:E.204, H:E.238, H:E.238, H:H.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ando, N. et al., Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-12-21

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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