SMTL ID : 5gg5.1

Crystal structure of Mycobacterium smegmatis MutT1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: R.189, H.190, G.194, R.196, R.206, R.238, K.317 Ligands: EDO.25 10 PLIP interactions: 10 interactions with chain A Water bridges: A:R.196, A:R.196, A:K.317, A:K.317 Salt bridges: A:R.189, A:H.190, A:R.196, A:R.206, A:R.238, A:K.317 SO4.2: 2 residues within 4Å: Chain A: R.198 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.198 SO4.3: 7 residues within 4Å: Chain A: R.196, R.204, R.236, T.261, E.262, E.263, Q.291 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:E.262, A:E.262, A:E.262, A:E.263, A:Q.291 Water bridges: A:R.196, A:R.196, A:R.196, A:R.196, A:R.204, A:R.204, A:R.238 Salt bridges: A:R.196, A:R.204, A:R.236 SO4.4: 6 residues within 4Å: Chain A: H.108, D.141, F.142, W.153 Ligands: EDO.18, EDO.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.142, A:W.153 Water bridges: A:G.140, A:D.141 Salt bridges: A:H.108 SO4.5: 3 residues within 4Å: Chain A: R.118, T.120, R.129 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.118, A:R.129 SO4.6: 7 residues within 4Å: Chain A: R.75, K.85, K.128 Ligands: SO4.7, EDO.17, EDO.21, EDO.22 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.75, A:Y.78 Salt bridges: A:R.75, A:K.128 SO4.7: 5 residues within 4Å: Chain A: K.87, I.123, K.128 Ligands: SO4.6, EDO.22 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.87, A:K.87 Salt bridges: A:K.87, A:K.128 SO4.8: 3 residues within 4Å: Chain A: D.209, K.210, R.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.210 Salt bridges: A:R.213 SO4.9: 3 residues within 4Å: Chain A: G.194, R.195 Ligands: EDO.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.195 Salt bridges: A:R.195 SO4.10: 5 residues within 4Å: Chain A: V.176, K.177, R.178, P.179 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) SO4.11: 4 residues within 4Å: Chain A: G.86, K.87, E.101 Ligands: EDO.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.87 Water bridges: A:K.85, A:E.101, A:E.101 Salt bridges: A:K.87

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

EDO.12: 4 residues within 4Å: Chain A: S.197, R.198, Y.199 Ligands: SO4.2 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: V.68, F.175, V.176, R.178 Ligands: SO4.10 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: K.177 Ligands: EDO.34 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: K.170, R.173 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: E.104, E.105, T.106, G.107, D.141, F.142, S.143, N.145 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: K.85, Y.121, Y.165, D.167, D.168 Ligands: SO4.6 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: F.142, L.151, W.153 Ligands: SO4.4, EDO.19 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: R.53 Ligands: SO4.4, EDO.18 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: R.198, Y.199 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain A: A.46, K.85, G.86, K.87, K.128, V.130 Ligands: SO4.6, SO4.11, EDO.22 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: Y.121, K.128 Ligands: SO4.6, SO4.7, EDO.21 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: P.296, I.299, E.300, P.310, T.313, W.321 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: W.52, V.111, L.112, G.113, K.136, V.180, T.182 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: R.189, R.196, E.262, G.292, K.293 Ligands: SO4.1 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: T.230, L.231, Y.232, Q.252, L.253, H.255 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: G.117, R.118, K.170, R.174, E.311 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain A: R.195, R.196 Ligands: SO4.9 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain A: P.76, R.77 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: W.81, Q.162, Q.164 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain A: K.210, R.213 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain A: L.277, A.280, G.281, G.328 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: M.224, G.227, A.228, T.229, L.250 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain A: K.177 Ligands: EDO.14 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain A: R.213, A.216, E.217, Q.241, P.245 Ligand excluded by PLIP

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.36: 7 residues within 4Å: Chain A: R.204, K.205, D.235, R.236, V.237, H.240, N.256 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.256 PEG.37: 2 residues within 4Å: Chain A: R.211, R.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.211, A:R.211, A:R.316, A:R.316 PEG.38: 7 residues within 4Å: Chain A: E.94, P.95, W.131, T.312, Y.335, L.336, S.337 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.94, A:T.312, A:S.337 Water bridges: A:R.45, A:R.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arif, S.M. et al., Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-04-19

Peptides

Hydrolase, NUDIX family protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hydrolase, NUDIX family protein

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