SMTL ID : 4r1r.5 (9 other biounits)

RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP AND EFFECTOR DTTP FROM ESCHERICHIA COLI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-6-6-mer

Ligands

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

TTP.1: 11 residues within 4Å: Chain A: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, T.276, F.281 Chain K: S.249 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.234, A:L.234, A:I.268, A:F.281 Hydrogen bonds: A:D.232, A:L.234, A:R.262, A:R.269, A:T.276 Salt bridges: A:R.262 TTP.3: 11 residues within 4Å: Chain C: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, T.276, F.281 Chain I: S.249 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.234, C:L.234, C:I.268, C:F.281 Hydrogen bonds: C:D.232, C:L.234, C:R.262, C:R.269, C:T.276 Salt bridges: C:R.262 TTP.5: 11 residues within 4Å: Chain E: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, T.276, F.281 Chain G: S.249 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:L.234, E:L.234, E:I.268, E:F.281 Hydrogen bonds: E:D.232, E:L.234, E:R.262, E:R.269, E:T.276 Salt bridges: E:R.262 TTP.7: 11 residues within 4Å: Chain E: S.249 Chain G: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, T.276, F.281 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:L.234, G:L.234, G:I.268, G:F.281 Hydrogen bonds: G:D.232, G:L.234, G:R.262, G:R.269, G:T.276 Salt bridges: G:R.262 TTP.9: 11 residues within 4Å: Chain C: S.249 Chain I: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, T.276, F.281 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:L.234, I:L.234, I:I.268, I:F.281 Hydrogen bonds: I:D.232, I:L.234, I:R.262, I:R.269, I:T.276 Salt bridges: I:R.262 TTP.11: 11 residues within 4Å: Chain A: S.249 Chain K: D.232, S.233, L.234, I.237, R.262, I.268, R.269, H.275, T.276, F.281 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:L.234, K:L.234, K:I.268, K:F.281 Hydrogen bonds: K:D.232, K:L.234, K:R.262, K:R.269, K:T.276 Salt bridges: K:R.262

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

GDP.2: 15 residues within 4Å: Chain A: T.209, P.210, S.224, C.225, G.253, N.437, 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 A Hydrogen bonds: A:T.209, A:T.209, A:T.209, A:T.209, A:N.437, A:E.623, A:T.624, A:T.624, A:T.624, A:S.625, A:S.625 GDP.4: 15 residues within 4Å: Chain C: T.209, P.210, S.224, C.225, G.253, N.437, 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:T.209, C:N.437, C:E.623, C:T.624, C:T.624, C:T.624, C:S.625, C:S.625 GDP.6: 15 residues within 4Å: Chain E: T.209, P.210, S.224, C.225, G.253, N.437, 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 E Hydrogen bonds: E:T.209, E:T.209, E:T.209, E:T.209, E:N.437, E:E.623, E:T.624, E:T.624, E:T.624, E:S.625, E:S.625 GDP.8: 15 residues within 4Å: Chain G: T.209, P.210, S.224, C.225, G.253, N.437, 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 G Hydrogen bonds: G:T.209, G:T.209, G:T.209, G:T.209, G:N.437, G:E.623, G:T.624, G:T.624, G:T.624, G:S.625, G:S.625 GDP.10: 15 residues within 4Å: Chain I: T.209, P.210, S.224, C.225, G.253, N.437, 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 I Hydrogen bonds: I:T.209, I:T.209, I:T.209, I:T.209, I:N.437, I:E.623, I:T.624, I:T.624, I:T.624, I:S.625, I:S.625 GDP.12: 15 residues within 4Å: Chain K: T.209, P.210, S.224, C.225, G.253, N.437, 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 K Hydrogen bonds: K:T.209, K:T.209, K:T.209, K:T.209, K:N.437, K:E.623, K:T.624, K:T.624, K:T.624, K:S.625, K:S.625

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eriksson, M. et al., Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding. Structure (1997)

Release Date

1998-01-28

Peptides

RIBONUCLEOTIDE REDUCTASE R1 PROTEIN: ACEGIK
RIBONUCLEOTIDE REDUCTASE R2 PROTEIN: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
C

E
C

G
C

I
C

K
C

B
F

D
F

F
F

H
F

J
F

L
F

RIBONUCLEOTIDE REDUCTASE R1 PROTEIN

RIBONUCLEOTIDE REDUCTASE R2 PROTEIN

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