SMTL ID : 6jcl.1 (3 other biounits)

Crystal structure of cofactor-bound Rv0187 from MTB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 21 residues within 4Å: Chain A: I.42, A.43, V.44, G.68, T.69, L.70, F.73, S.74, L.91, E.92, Y.93, Q.94, H.97, G.119, P.120, A.121, F.137, D.139, A.140, D.141, Y.148 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.70 Hydrogen bonds: A:V.44, A:L.70, A:F.73, A:S.74, A:S.74, A:Y.93, A:H.97, A:A.121, A:D.139, A:D.139, A:D.141, A:D.141 Water bridges: A:N.144, A:N.144, A:N.144 pi-Stacking: A:Y.93 SAH.6: 21 residues within 4Å: Chain B: I.42, A.43, V.44, G.68, T.69, L.70, F.73, S.74, L.91, E.92, Y.93, Q.94, H.97, G.119, P.120, A.121, F.137, D.139, A.140, D.141, Y.148 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.70 Hydrogen bonds: B:V.44, B:L.70, B:F.73, B:S.74, B:S.74, B:Y.93, B:H.97, B:A.121, B:D.139, B:D.141, B:D.141 Water bridges: B:T.69, B:N.144, B:Y.148

5 x SR: STRONTIUM ION(Non-functional Binders)

SR.2: 3 residues within 4Å: Chain A: D.139, D.165, N.166 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.139, A:D.139, A:D.165, H2O.2 SR.4: 2 residues within 4Å: Chain A: D.179, D.181 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.179, A:D.181, A:D.181 SR.5: 1 residues within 4Å: Chain A: D.178 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, H2O.3 SR.7: 3 residues within 4Å: Chain B: D.139, D.165, N.166 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.139, B:D.139, B:D.165, H2O.8 SR.11: 1 residues within 4Å: Chain B: D.178 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.178, H2O.7

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 9 residues within 4Å: Chain A: V.44, Q.48, F.51, L.52, F.137, V.163, D.165, F.214 Chain B: I.203 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:I.203, A:V.44, A:Q.48, A:L.52, A:F.137, A:F.137, A:V.163, A:F.214, A:F.214 Hydrogen bonds: A:Q.48, A:D.165 Water bridges: A:N.166, A:T.205, A:T.205 MPD.8: 9 residues within 4Å: Chain A: I.203 Chain B: V.44, Q.48, F.51, L.52, F.137, V.163, D.165, F.214 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.44, B:L.52, B:F.137, B:F.137, B:V.163, B:F.214, B:F.214, A:I.203 Hydrogen bonds: B:Q.48, B:D.165 Water bridges: B:N.166, B:T.205, B:T.205 MPD.9: 2 residues within 4Å: Chain B: Q.150, W.151 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.151 Hydrogen bonds: B:A.147

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 4 residues within 4Å: Chain B: M.192, G.193, H.195, L.198 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.198 Water bridges: B:D.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S. et al., Structural and biochemical characterization of Rv0187, an O-methyltransferase from Mycobacterium tuberculosis. Sci Rep (2019)

Release Date

2019-12-11

Peptides

Probable O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable O-methyltransferase

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