SMTL ID : 1xjg.1

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP-UDP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.142 Ligands: DTP.3 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: D.141 Ligands: DTP.6 No protein-ligand interaction detected (PLIP)

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 16 residues within 4Å: Chain A: Y.27, N.90, S.91, A.133, G.161, G.162, N.320, P.321, C.322, E.324, A.489, P.490, T.491, G.492, S.493, I.494 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.91, A:A.133, A:C.322, A:T.491, A:T.491, A:G.492, A:S.493, A:I.494 UDP.5: 17 residues within 4Å: Chain B: N.90, S.91, A.133, C.134, G.161, G.162, Q.203, 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 B Hydrogen bonds: B:S.91, B:A.133, B:Q.203, B:Q.203, B:N.320, B:C.322, B:T.491, B:G.492, B:S.493, B:S.493, B:I.494 Water bridges: B:G.162, B:G.162

2 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.3: 18 residues within 4Å: Chain A: D.141, S.142, I.143, I.146, R.171, V.177, A.178, G.179, T.180, K.183, A.184, S.185, F.190 Chain B: K.158, V.200, V.201, K.202 Ligands: MG.1 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:K.202, B:K.202, A:D.141, A:R.171, A:A.178, A:T.180, A:S.185 Salt bridges: B:K.158, B:K.158, A:R.171, A:R.171 Hydrophobic interactions: A:I.143, A:I.146, A:F.190 DTP.6: 18 residues within 4Å: Chain A: H.127, K.158, V.200, V.201, K.202 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.4 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.143, B:I.146, B:F.190 Hydrogen bonds: B:D.141, B:I.143, B:A.178, B:G.179, B:S.185, A:K.202, A:K.202 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

2005-12-20

Peptides

ribonucleotide reductase, B12-dependent: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ribonucleotide reductase, B12-dependent

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