SMTL ID : 1xjk.1

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dGTP-ADP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: DGT.3 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: DGT.6 No protein-ligand interaction detected (PLIP)

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 19 residues within 4Å: Chain A: N.90, S.91, A.133, C.134, G.160, G.161, G.162, K.202, A.210, N.320, P.321, C.322, E.324, A.489, P.490, T.491, G.492, S.493, I.494 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.91, A:S.91, A:K.202, A:K.202, A:A.210, A:N.320, A:C.322, A:E.324, A:T.491, A:G.492, A:S.493, A:I.494 Water bridges: A:S.91 ADP.5: 16 residues within 4Å: Chain B: N.90, S.91, A.133, G.161, G.162, K.202, N.320, P.321, C.322, E.324, A.489, P.490, T.491, G.492, S.493, I.494 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.91, B:S.91, B:S.91, B:K.202, B:N.320, B:C.322, B:E.324, B:T.491, B:G.492, B:S.493, B:I.494

2 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.3: 15 residues within 4Å: Chain A: D.141, S.142, I.143, I.146, R.171, V.177, A.178, A.184, S.185, F.190 Chain B: K.158, V.200, V.201, Q.203 Ligands: MG.1 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.143, A:I.146 Hydrogen bonds: A:D.141, A:I.143, A:R.171, A:A.178, A:A.178, A:S.185, A:S.185, B:V.201 Water bridges: A:E.144, A:R.171, A:R.171 Salt bridges: A:R.171, A:R.171, B:K.158, B:K.158 DGT.6: 15 residues within 4Å: Chain A: H.127, L.128, K.158, V.200, V.201 Chain B: D.141, S.142, I.143, R.171, V.177, A.178, A.184, S.185, F.190 Ligands: MG.4 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.143 Hydrogen bonds: B:D.141, B:I.143, B:A.178, B:S.185, B:S.185, A:V.201 Water bridges: B:E.144, B:R.171, B:R.171 Salt bridges: B:R.171, A:H.127, A:K.158, A:K.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsson, K.-M. et al., Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase. Nat.Struct.Mol.Biol. (2004)

Release Date

2005-11-22

Peptides

ribonucleotide reductase, B12-dependent: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ribonucleotide reductase, B12-dependent