SMTL ID : 5xd5.1

Crystal structure of Mycobacterium smegmatis MutT1 in complex with ATP, magnesium fluoride and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: R.75, R.77, Y.78, K.85, G.86, K.87, Y.121, I.123, K.128, E.147, Y.165, D.168 Ligands: PO4.2, MG.7, MG.10, F.11, F.12, F.13 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.87, A:Y.121, A:Y.165, A:D.168 Water bridges: A:K.85, A:D.167, A:D.168 Salt bridges: A:R.75, A:R.75, A:R.75, A:R.77, A:K.85, A:K.85, A:K.85, A:K.87, A:K.87, A:K.128, A:K.128, A:K.128 pi-Stacking: A:Y.121, A:Y.165, A:Y.165 ATP.17: 15 residues within 4Å: Chain B: R.75, Y.78, K.85, G.86, K.87, E.105, Y.121, K.128, E.147, Y.165, D.168 Ligands: MG.21, MG.24, F.25, F.27 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:Y.78, B:D.168 Water bridges: B:R.75, B:R.75, B:K.85, B:K.87, B:Y.121, B:Y.121, B:Y.132, B:D.167 Salt bridges: B:R.75, B:R.75, B:R.75, B:K.85, B:K.85, B:K.85, B:K.87, B:K.87, B:K.128, B:K.128, B:K.128 pi-Stacking: B:Y.121, B:Y.121, B:Y.165, B:Y.165

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 9 residues within 4Å: Chain A: R.77, K.87, E.147 Ligands: ATP.1, MG.9, MG.10, F.11, F.12, F.13 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.77, A:K.87

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.115, W.131, W.133, Y.335, L.336, S.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.115, A:S.337 Water bridges: A:E.94, A:E.94 GOL.4: 5 residues within 4Å: Chain A: R.204, D.235, R.236, V.237, H.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.204, A:D.235, A:D.235 Water bridges: A:H.240 GOL.5: 6 residues within 4Å: Chain A: R.45, L.88, D.89, Q.90, G.91, E.92 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:L.88, A:Q.90, A:G.91, A:E.92, A:E.92 Water bridges: A:R.45, A:R.45, A:R.45 GOL.6: 6 residues within 4Å: Chain A: I.295, P.296, T.313, G.314, N.315, W.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.313, A:W.321 GOL.18: 7 residues within 4Å: Chain B: R.115, W.131, W.133, T.312, Y.335, L.336, S.337 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.115, B:T.312, B:S.337 Water bridges: B:E.94, B:S.337, B:K.342 GOL.19: 3 residues within 4Å: Chain B: D.235, R.236, H.240 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.235, B:D.235 Water bridges: B:V.237, B:N.256 GOL.20: 1 residues within 4Å: Chain B: D.146 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.146

8 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 9 residues within 4Å: Chain A: R.75, K.85, G.86, E.105, E.147 Ligands: ATP.1, MG.8, MG.10, F.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.85, A:E.105, A:E.147, H2O.4 MG.8: 9 residues within 4Å: Chain A: E.101, E.105, E.147 Ligands: MG.7, MG.9, MG.10, F.11, F.12, F.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.101, A:E.105, A:E.147, H2O.5 MG.9: 7 residues within 4Å: Chain A: E.101 Ligands: PO4.2, MG.8, MG.10, F.11, F.12, F.13 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.101, H2O.2, H2O.3, H2O.5 MG.10: 10 residues within 4Å: Chain A: K.87, E.147 Ligands: ATP.1, PO4.2, MG.7, MG.8, MG.9, F.11, F.12, F.13 No protein-ligand interaction detected (PLIP) MG.21: 8 residues within 4Å: Chain B: K.85, G.86, E.105, E.147 Ligands: ATP.17, MG.22, MG.24, F.25 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.85, B:E.105, B:E.147, H2O.14 MG.22: 9 residues within 4Å: Chain B: E.101, E.105, E.147 Ligands: MG.21, MG.23, MG.24, F.25, F.26, F.27 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.101, B:E.105, B:E.147, H2O.12 MG.23: 8 residues within 4Å: Chain B: R.100, E.101, E.104 Ligands: MG.22, MG.24, F.25, F.26, F.27 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.101, H2O.12, H2O.13 MG.24: 9 residues within 4Å: Chain B: K.87, E.147 Ligands: ATP.17, MG.21, MG.22, MG.23, F.25, F.26, F.27 No protein-ligand interaction detected (PLIP)

6 x F: FLUORIDE ION(Non-covalent)

F.11: 13 residues within 4Å: Chain A: K.85, G.86, E.101, E.105, E.147 Ligands: ATP.1, PO4.2, MG.7, MG.8, MG.9, MG.10, F.12, F.13 No protein-ligand interaction detected (PLIP) F.12: 9 residues within 4Å: Chain A: E.101, E.147 Ligands: ATP.1, PO4.2, MG.8, MG.9, MG.10, F.11, F.13 No protein-ligand interaction detected (PLIP) F.13: 10 residues within 4Å: Chain A: G.86, K.87, E.101 Ligands: ATP.1, PO4.2, MG.8, MG.9, MG.10, F.11, F.12 No protein-ligand interaction detected (PLIP) F.25: 12 residues within 4Å: Chain B: K.85, G.86, E.101, E.105, E.147 Ligands: ATP.17, MG.21, MG.22, MG.23, MG.24, F.26, F.27 No protein-ligand interaction detected (PLIP) F.26: 7 residues within 4Å: Chain B: E.101, E.147 Ligands: MG.22, MG.23, MG.24, F.25, F.27 No protein-ligand interaction detected (PLIP) F.27: 9 residues within 4Å: Chain B: G.86, K.87, E.101 Ligands: ATP.17, MG.22, MG.23, MG.24, F.25, F.26 No protein-ligand interaction detected (PLIP)

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

CL.14: 3 residues within 4Å: Chain A: H.190, R.206, R.238 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain A: W.302, R.305, A.306, E.329, L.330 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: R.189, R.316, K.317 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: H.190, R.206, R.238 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain B: R.236, E.262, E.263, Q.291 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: R.204, R.236, E.263 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain B: R.316, K.317 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arif, S.M. et al., Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1. J. Struct. Biol. (2017)

Release Date

2017-08-09

Peptides

Hydrolase, NUDIX family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Hydrolase, NUDIX family protein

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