SMTL ID : 6zma.1

Structure of the tRNA-Monooxygenase enzyme MiaE frozen under 140 bar of krypton using the soak and freeze methodology

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: E.38, E.69, H.72, E.151 Ligands: FE.2, TRS.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.38, A:E.69, A:H.72, H2O.1, H2O.2 FE.2: 6 residues within 4Å: Chain A: E.69, E.122, E.151, H.154 Ligands: FE.1, TRS.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.69, A:E.122, A:E.151, A:H.154, H2O.2 FE.14: 6 residues within 4Å: Chain B: E.38, E.69, H.72, E.151 Ligands: FE.15, TRS.16 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.38, B:E.69, B:H.72, H2O.5, H2O.6 FE.15: 6 residues within 4Å: Chain B: E.69, E.122, E.151, H.154 Ligands: FE.14, TRS.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.69, B:E.122, B:E.151, B:H.154, H2O.6

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

CL.3: 2 residues within 4Å: Chain A: R.67 Chain B: R.67 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: D.8, L.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:L.11, H2O.2 CA.5: 1 residues within 4Å: Chain A: G.84 No protein-ligand interaction detected (PLIP)

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 13 residues within 4Å: Chain A: C.37, E.38, A.41, E.69, I.121, E.122, S.125, E.151, H.196 Ligands: FE.1, FE.2, PEG.9, KR.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125, A:E.151, A:E.151 TRS.16: 13 residues within 4Å: Chain B: C.37, E.38, A.41, E.69, I.121, E.122, S.125, E.151, H.196 Ligands: FE.14, FE.15, PEG.20, KR.21 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.37, B:E.69, B:S.125, B:S.125 Water bridges: B:H.154

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

PEG.7: 6 residues within 4Å: Chain A: H.72, Q.75, R.142, F.143, G.146, L.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.75, A:R.142 PEG.8: 3 residues within 4Å: Chain A: G.98, E.184, L.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.98, A:S.188, A:S.188 PEG.9: 8 residues within 4Å: Chain A: C.37, K.40, A.41, T.44, R.100, I.121, H.196 Ligands: TRS.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.100, A:Y.158 Water bridges: A:A.96, A:Y.158 PEG.17: 6 residues within 4Å: Chain A: R.64, R.67 Chain B: E.74, Q.75, R.78 Ligands: EDO.25 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.67, B:R.78, B:R.78 Water bridges: A:R.67 PEG.18: 6 residues within 4Å: Chain B: E.68, H.72, Q.75, G.146, L.147, S.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.68, B:E.68, B:Q.75 PEG.19: 4 residues within 4Å: Chain B: R.64, R.67, E.68, V.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.67, B:R.67 PEG.20: 8 residues within 4Å: Chain B: A.41, T.44, R.100, T.114, G.118, I.121, Y.158 Ligands: TRS.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.100, B:R.100, B:T.114

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.10: 7 residues within 4Å: Chain A: F.39, S.43, A.50 Chain B: F.39, S.43, S.47, A.50 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.43, A:S.43 Water bridges: A:S.43

6 x KR: KRYPTON(Non-covalent)(Covalent)

KR.11: 4 residues within 4Å: Chain A: H.34, F.129, F.195 Ligands: TRS.6 No protein-ligand interaction detected (PLIP) KR.12: 4 residues within 4Å: Chain A: Q.27, L.30, L.140, Y.144 No protein-ligand interaction detected (PLIP) KR.21: 7 residues within 4Å: Chain B: H.34, S.125, F.129, E.151, F.195 Ligands: TRS.16, KR.22 No protein-ligand interaction detected (PLIP) KR.22: 5 residues within 4Å: Chain B: H.34, F.129, F.195 Ligands: KR.21, KR.23 No protein-ligand interaction detected (PLIP) KR.23: 5 residues within 4Å: Chain B: L.30, H.34, Y.144 Ligands: KR.22, KR.24 No protein-ligand interaction detected (PLIP) KR.24: 5 residues within 4Å: Chain B: Q.27, L.30, L.140, Y.144 Ligands: KR.23 No protein-ligand interaction detected (PLIP)

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

EDO.13: 2 residues within 4Å: Chain A: Q.75, R.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.75 EDO.25: 5 residues within 4Å: Chain B: Q.75, L.79, R.82, F.143 Ligands: PEG.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.82, B:E.139 EDO.26: 5 residues within 4Å: Chain B: L.24, A.25, D.26, Q.27, E.28 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.25, B:Q.27 Water bridges: B:R.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carpentier, P. et al., Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. Nucleic Acids Res. (2020)

Release Date

2020-09-02

Peptides

tRNA hydroxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

tRNA hydroxylase