SMTL ID : 3o0n.1

Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP and Adenosylcobalamin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

TTP.1: 16 residues within 4Å: Chain A: D.141, S.142, I.143, I.146, R.171, V.177, A.178, G.179, A.184, S.185, F.190 Chain B: K.158, V.200, V.201, K.202 Ligands: MG.4 22 PLIP interactions: 15 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.143, A:I.143, A:I.146, A:F.190, B:K.158 Hydrogen bonds: A:D.141, A:I.143, A:R.171, A:A.178, A:G.179, A:S.185, B:V.200, B:K.202 Water bridges: A:E.144, A:R.171, A:R.171, B:K.158, B:K.158 Salt bridges: A:R.171, A:R.171, B:K.158, B:K.158 TTP.6: 16 residues within 4Å: Chain A: K.158, V.200, V.201 Chain B: D.141, S.142, I.143, I.146, R.171, V.177, A.178, G.179, K.183, A.184, S.185, F.190 Ligands: MG.5 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.143, B:I.143, B:I.146, B:V.177, B:F.190, A:K.158 Hydrogen bonds: B:D.141, B:I.143, B:R.171, B:A.178, B:G.179, B:S.185, A:V.200 Water bridges: B:E.144, B:R.171, B:R.171, A:K.158, A:K.158, A:K.158 Salt bridges: B:R.171, A:K.158, A:K.158

1 x CO: COBALT (II) ION(Non-functional Binders)

CO.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: T.606, V.607 Ligand excluded by PLIP

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

MG.4: 1 residues within 4Å: Ligands: TTP.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: TTP.6 No protein-ligand interaction detected (PLIP)

1 x B12: COBALAMIN(Non-covalent)

B12.7: 19 residues within 4Å: Chain B: R.26, N.242, G.294, D.295, C.322, P.490, G.492, S.493, S.502, F.508, R.514, T.598, N.600, T.626, V.627, Y.628, D.630, L.633 Ligands: 5AD.8 15 PLIP interactions: 14 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:P.490, B:F.508, B:Y.628, B:L.633 Hydrogen bonds: B:S.502, B:E.505, B:R.514, B:R.514, B:N.600, B:V.627, B:D.630, B:D.630 Water bridges: B:T.598, B:V.627 Metal complexes: B12.7

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.8: 13 residues within 4Å: Chain B: M.212, N.242, L.243, S.244, G.297, P.321, C.322, G.323, P.490, S.596, T.598, T.626 Ligands: B12.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.244, B:D.295, B:D.295, B:G.297, B:S.596 Water bridges: B:T.319, B:C.322, B:T.626, B:T.626, B:T.626

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsson, K.M. et al., Structural Basis for Adenosylcobalamin Activation in AdoCbl-Dependent Ribonucleotide Reductases. Acs Chem.Biol. (2010)

Release Date

2010-07-28

Peptides

Ribonucleoside-diphosphate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase

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