SMTL ID : 1xje.1

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

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

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

GDP.2: 20 residues within 4Å: Chain A: N.90, S.91, A.133, G.160, G.161, G.162, R.207, R.208, A.210, N.320, P.321, C.322, E.324, L.335, A.489, P.490, T.491, G.492, S.493, I.494 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.91, A:S.91, A:G.161, A:R.207, A:R.208, 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:R.207, A:R.207 Salt bridges: A:R.207 pi-Cation interactions: A:R.207, A:R.207 GDP.5: 21 residues within 4Å: Chain B: N.90, S.91, A.133, G.160, G.161, G.162, R.207, R.208, G.209, A.210, N.320, P.321, C.322, E.324, L.335, A.489, P.490, T.491, G.492, S.493, I.494 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:S.91, B:S.91, B:G.161, B:R.207, B:R.208, B:A.210, B:N.320, B:C.322, B:E.324, B:T.491, B:G.492, B:S.493, B:I.494 Water bridges: B:G.162, B:G.162, B:R.207, B:R.207 Salt bridges: B:R.207 pi-Cation interactions: B:R.207, B:R.207

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

TTP.3: 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.1 21 PLIP interactions: 13 interactions with chain A, 8 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: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, B:K.158 Salt bridges: A:R.171, B:K.158, B:K.158 TTP.6: 17 residues within 4Å: Chain A: 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, T.180, A.184, S.185, F.190 Ligands: MG.4 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.143, B:I.146, B:V.177, B:T.180, 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, A:K.202 Water bridges: B:S.142, B:E.144, B:G.186 Salt bridges: B:R.171, A:K.158, A:K.158

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: E.144 Chain B: H.127, L.155, K.158 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.127, B:H.127, B:K.158, B: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

2005-10-11

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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