SMTL ID : 8j8j.1

Membrane bound PRTase, C3 symmetry, donor bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.1: 15 residues within 4Å: Chain A: R.22, K.28, V.69, Y.70, N.73, D.77, K.87, R.90, Y.131, Q.135, Y.138, K.143, Y.157, R.160 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.22, A:Y.70, A:Y.70, A:N.73, A:N.73, A:Y.131, A:Q.135, A:Y.138, A:Y.138, A:Y.157 Salt bridges: A:R.22, A:K.28, A:K.87, A:R.90, A:K.143, A:R.160 PRP.4: 15 residues within 4Å: Chain B: R.22, K.28, V.69, Y.70, N.73, D.77, K.87, R.90, Y.131, Q.135, Y.138, K.143, Y.157, R.160 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.22, B:Y.70, B:Y.70, B:N.73, B:N.73, B:Y.131, B:Q.135, B:Y.138, B:Y.138, B:Y.157 Salt bridges: B:R.22, B:K.28, B:K.87, B:R.90, B:K.143, B:R.160 PRP.7: 14 residues within 4Å: Chain C: R.22, K.28, V.69, Y.70, N.73, K.87, R.90, Y.131, Q.135, Y.138, K.143, Y.157, R.160 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:R.22, C:Y.70, C:Y.70, C:N.73, C:N.73, C:Y.131, C:Q.135, C:Y.138, C:Y.138, C:Y.157 Salt bridges: C:R.22, C:K.28, C:K.87, C:R.90, C:K.143, C:R.160

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.73, D.77 Ligands: PRP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.77 MG.5: 3 residues within 4Å: Chain B: N.73, D.77 Ligands: PRP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.77 MG.8: 3 residues within 4Å: Chain C: N.73, D.77 Ligands: PRP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.77

3 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.3: 15 residues within 4Å: Chain A: L.126, V.127, M.134, S.155, I.159, I.162, V.166, P.171, L.172, L.177 Chain B: G.245, S.246, A.249, M.252, I.253 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.253, A:L.126, A:I.159, A:I.162 Hydrogen bonds: B:S.246, A:L.172 PGW.6: 15 residues within 4Å: Chain B: L.126, V.127, M.134, S.155, I.159, I.162, V.166, P.171, L.172, L.177 Chain C: G.245, S.246, A.249, M.252, I.253 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.126, B:I.159, B:I.162, C:I.253 Hydrogen bonds: B:L.172, C:S.246 PGW.9: 15 residues within 4Å: Chain A: G.245, S.246, A.249, M.252, I.253 Chain C: L.126, V.127, M.134, S.155, I.159, I.162, V.166, P.171, L.172, L.177 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.126, C:I.159, C:I.162, A:I.253 Hydrogen bonds: C:L.172, A:S.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, S. et al., Structural analysis of phosphoribosyltransferase-mediated cell wall precursor synthesis in Mycobacterium tuberculosis. Nat Microbiol (2024)

Release Date

2024-02-07

Peptides

Decaprenyl-phosphate phosphoribosyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

Membrane

We predict this structure to be a membrane protein.
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Decaprenyl-phosphate phosphoribosyltransferase