SMTL ID : 4erp.2 (1 other biounit)

Crystal structure of a gemcitabine-diphosphate inhibited E. coli class Ia ribonucleotide reductase complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.45 Å

Oligo State

hetero-4-4-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 15 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, F.87, K.91 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.10, A:D.11, A:E.15, A:R.16, A:N.18, A:K.21, A:T.55 Salt bridges: A:K.9, A:R.10, A:H.59, A:K.91 ATP.2: 15 residues within 4Å: Chain B: 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, F.87, K.91 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.10, B:R.10, B:D.11, B:E.15, B:R.16, B:N.18, B:K.21, B:T.55 Salt bridges: B:K.9, B:R.10, B:K.91 ATP.5: 15 residues within 4Å: Chain E: 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, F.87, K.91 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:R.10, E:D.11, E:R.16, E:N.18, E:K.21, E:T.55 Salt bridges: E:K.9, E:R.10, E:H.59, E:K.91 ATP.6: 15 residues within 4Å: Chain F: 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, F.87, K.91 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:R.10, F:R.10, F:D.11, F:R.16, F:N.18, F:K.21, F:T.55 Salt bridges: F:K.9, F:R.10, F:K.91

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

FEO.3: 6 residues within 4Å: Chain C: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 6 interactions with chain C, 2 Ligand-Water interactions, Metal complexes: C:D.84, C:E.115, C:E.115, C:H.118, C:E.204, C:E.238, H2O.1, H2O.1 FEO.4: 6 residues within 4Å: Chain D: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 8 interactions with chain D, Metal complexes: D:D.84, D:D.84, D:E.115, D:E.115, D:H.118, D:E.204, D:E.238, D:H.241 FEO.7: 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:E.238, H2O.1, H2O.1 FEO.8: 6 residues within 4Å: Chain H: D.84, E.115, H.118, E.204, E.238, H.241 8 PLIP interactions: 8 interactions with chain H, Metal complexes: H:D.84, H:D.84, H:E.115, H:E.115, H:H.118, H:E.204, H:E.238, H:H.241

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: ABEF
Ribonucleoside-diphosphate reductase 1 subunit beta: CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

E
C

F
D

C
E

D
G

G
E

H
G

Ribonucleoside-diphosphate reductase 1 subunit alpha

Ribonucleoside-diphosphate reductase 1 subunit beta

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