SMTL ID : 6w4x.1

Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 12 residues within 4Å: Chain A: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, F.281 Chain B: S.249, C.292 Ligands: MG.2 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.234, A:L.234, A:I.268, A:F.281 Hydrogen bonds: A:D.232, A:L.234, A:R.269, B:C.292 Salt bridges: A:R.262 TTP.4: 15 residues within 4Å: Chain A: S.249, R.251, C.292 Chain B: D.232, S.233, L.234, I.237, I.261, R.262, I.268, R.269, G.270, H.275, F.281 Ligands: MG.5 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.234, B:L.234, B:I.268, B:F.281 Hydrogen bonds: B:L.234, B:R.269, B:G.270, A:R.251, A:R.251, A:C.292 Salt bridges: B:R.262, B:R.262, B:R.269

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

MG.2: 1 residues within 4Å: Ligands: TTP.1 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: R.262 Ligands: TTP.4 No protein-ligand interaction detected (PLIP)

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 22 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, L.438, C.439, E.441, L.464, P.621, S.622, E.623, T.624, S.625 Chain C: Q.350, E.351 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Y.155, B:T.209, B:T.209, B:A.252, B:G.299, B:A.301, B:N.437, B:L.438, B:C.439, B:E.441, B:S.622, B:E.623, B:T.624, B:S.625, B:S.625 Salt bridges: B:R.298 pi-Cation interactions: B:R.298, B:R.298

2 x FEO: MU-OXO-DIIRON(Covalent)

FEO.6: 7 residues within 4Å: Chain C: D.85, E.116, H.119, X.123, E.205, E.239, H.242 8 PLIP interactions: 5 interactions with chain C, 3 Ligand-Water interactions, Metal complexes: C:D.85, C:E.116, C:E.116, C:E.205, C:H.242, H2O.1, H2O.1, H2O.1 FEO.7: 7 residues within 4Å: Chain D: D.85, W.112, E.116, H.119, E.205, E.239, H.242 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Water interactions, Metal complexes: D:E.116, D:E.116, D:H.119, D:E.205, D:E.239, D:E.239, D:H.242, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, G. et al., Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex. Science (2020)

Release Date

2020-04-08

Peptides

Ribonucleoside-diphosphate reductase 1 subunit alpha: AB
Ribonucleoside-diphosphate reductase 1 subunit beta: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ribonucleoside-diphosphate reductase 1 subunit alpha

Ribonucleoside-diphosphate reductase 1 subunit beta

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