SMTL ID : 6m69.1

Crystal structure of Mycobacterium smegmatis MutT1 in complex with GMPPCP (GDP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

GDP.1: 8 residues within 4Å: Chain A: R.75, Y.78, K.85, Y.121, I.123, K.128, Y.165 Ligands: MG.5 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:Y.78, A:K.85 Water bridges: A:R.75, A:R.75, A:R.75, A:R.77, A:S.82, A:K.87, A:K.128, A:Y.165, A:Y.165 Salt bridges: A:R.75, A:R.75, A:K.85, A:K.128, A:K.128 pi-Stacking: A:Y.121, A:Y.121, A:Y.165 pi-Cation interactions: A:Y.121

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 10 residues within 4Å: Chain A: R.189, H.190, R.196, R.206, R.238, E.262, Q.291, G.292, K.317 Ligands: EDO.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:E.262, A:Q.291, A:G.292 Water bridges: A:R.196, A:R.206, A:E.262, A:K.317 Salt bridges: A:R.189, A:H.190, A:H.190, A:R.196, A:R.196, A:R.206, A:R.238, A:R.238, A:K.317

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: R.189, K.317 Ligands: POP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.189, A:R.189, A:K.317, A:K.317 Water bridges: A:N.315 EDO.4: 6 residues within 4Å: Chain A: V.111, L.112, T.182, K.183, T.184, N.285 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.112, A:T.184, A:N.285 Water bridges: A:T.182, A:T.182, A:N.285

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: R.75, K.85, Y.121 Ligands: GDP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raj, P. et al., Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-10-14

Peptides

Hydrolase, NUDIX family protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hydrolase, NUDIX family protein

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