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Ligand · RFP

RFP · Rifampicin

RFP, Rifampicin (C43 H58 N4 O12, 823.0 g/mol), in the MolNFT structures on GenesisL1: bound in 26 records (15 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands found with it.

Component
RFP
Formula
C43 H58 N4 O12
Class
ligand
Structures
26
PDB entries
15

Binding sites

RFP in 26 structures; the first of them:

  • 5HV1 · Rifampin phosphotransferase in complex with AMPPNP and rifampin from Listeria… · RFP A902 · binds ILE331, VAL333, GLN336, TYR351, THR354, THR355, PRO356, ALA357 and 9 more
  • 5KOX · Structure of rifampicin monooxygenase complexed with rifampicin · RFP A502 · binds ARG43, GLY44, PHE69, PHE74, VAL93, ARG196, LEU200, ARG201 and 8 more
  • 5UAC · Escherichia coli RNA polymerase and Rifampin complex, wild-type · RFP C3001 · binds SER509, GLN510, SER512, GLN513, PHE514, ASP516, HIS526, ARG529 and 6 more
  • 5UAH · Escherichia coli RNA polymerase and Rifampin complex, RpoB D516V mutant · RFP C3001 · binds ARG143, SER509, GLN510, LEU511, SER512, GLN513, PHE514, VAL516 and 7 more
  • 5UAL · Escherichia coli RNA polymerase and Rifampin complex, RpoB S531L mutant · RFP C3001 · binds ARG143, SER509, GLN510, LEU511, SER512, GLN513, PHE514, MET515 and 8 more
  • 5UHB · Crystal structure of Mycobacterium tuberculosis transcription initiation complex in… · RFP C1201 · binds ARG173, VAL176, SER434, GLN435, LEU436, SER437, GLN438, PHE439 and 12 more
  • 5UHC · Crystal structure of Mycobacterium tuberculosis transcription initiation complex… · RFP C1201 · binds ARG173, VAL176, SER434, GLN435, LEU436, SER437, GLN438, PHE439 and 20 more
  • 5UHD · Crystal structure of Mycobacterium tuberculosis transcription initiation complex… · RFP C1201 · binds ARG173, VAL176, SER434, GLN435, LEU436, SER437, GLN438, PHE439 and 14 more
  • 5UHG · Crystal structure of Mycobacterium tuberculosis transcription initiation complex in… · RFP C1201 · binds ARG173, VAL176, SER434, GLN435, LEU436, SER437, GLN438, PHE439 and 13 more
  • 6BED · Crystal structure of VACV D13 in complex with Rifampicin · RFP C601 · binds GLN27, GLU165, PHE168, PRO483, PHE486, PHE487, VAL24, PRO483 and 6 more
  • 6BRD · Crystal structure of rifampin monooxygenase from Streptomyces venezuelae, complexed with… · RFP A502 · binds GLN43, GLY44, HIS46, VAL69, VAL71, GLY73, PHE74, VAL93 and 17 more
  • 7SZJ · Cryo-EM structure of Rifamycin bound to E. coli RNAP and rrnBP1 promoter complex · RFP C3001 · binds ARG143, VAL146, SER509, GLN510, LEU511, SER512, GLN513, PHE514 and 13 more
  • 8K1N · mycobacterial efflux pump, substrate-bound state · RFP C601 · binds VAL55, TYR56, SER59, VAL63, GLN83, LEU86, TYR87, TRP101 and 12 more
  • 5KOX · Structure of rifampicin monooxygenase complexed with rifampicin · RFP A502 · binds ARG43, GLY44, PHE69, PHE74, VAL93, ARG196, LEU200, ARG201 and 8 more
  • 5UAC · Escherichia COLI RNA polymerase and rifampin complex, wild-type · RFP C3001 · binds SER509, GLN510, SER512, GLN513, PHE514, ASP516, HIS526, ARG529 and 6 more
  • 5UAH · Escherichia COLI RNA polymerase and rifampin complex, rpob D516V mutant · RFP C3001 · binds ARG143, SER509, GLN510, LEU511, SER512, GLN513, PHE514, VAL516 and 7 more
  • 5UAL · Escherichia COLI RNA polymerase and rifampin complex, rpob S531L mutant · RFP C3001 · binds GLN510, SER512, GLN513, PHE514, ASP516, HIS526, ARG529, LEU531 and 4 more
  • 5UH6 · Crystal structure of mycobacterium tuberculosis transcription initiation complex… · RFP C1201 · binds ARG173, GLN435, LEU436, SER437, GLN438, PHE439, ASP441, HIS451 and 11 more
  • 5UHB · Crystal structure of mycobacterium tuberculosis transcription initiation complex in… · RFP C1201 · binds SER434, GLN435, LEU436, SER437, GLN438, PHE439, ASP441, HIS451 and 9 more
  • 5UHC · Crystal structure of mycobacterium tuberculosis transcription initiation complex… · RFP C1201 · binds SER434, GLN435, LEU436, SER437, GLN438, PHE439, ASP441, HIS451 and 15 more
  • 5UHD · Crystal structure of mycobacterium tuberculosis transcription initiation complex… · RFP C1201 · binds ARG173, GLN435, LEU436, GLN438, PHE439, ASP441, HIS451, ARG454 and 9 more
  • 5UHG · Crystal structure of mycobacterium tuberculosis transcription initiation complex in… · RFP C1201 · binds ARG173, SER434, GLN435, LEU436, GLN438, PHE439, ASP441, HIS451 and 10 more
  • 6BED · Crystal structure of vacv D13 in complex with rifampicin · RFP C601 · binds GLN27, GLU165, PRO483, PHE486, PHE487, VAL24, PHE486, VAL24 and 4 more
  • 6BRD · Crystal structure of rifampin monooxygenase from streptomyces venezuelae, complexed with… · RFP A502 · binds GLN43, GLY44, HIS46, VAL69, PHE74, VAL93, LEU176, MET192 and 12 more
  • 6CCV · Crystal structure of a mycobacterium smegmatis RNA polymerase transcription initiation… · RFP C1205 · binds SER425, GLN426, SER428, GLN429, PHE430, ASP432, HIS442, ARG445 and 8 more
  • 7SZJ · Cryo-EM structure of rifamycin bound to E. COLI rnap and RRNBP1 promoter complex · RFP C3001 · binds SER509, GLN510, LEU511, GLN513, PHE514, ASP516, HIS526, ARG529 and 7 more

Residues it binds most

ARG 26, GLN 28, PHE 30, SER 20, LEU 27, VAL 19, GLY 14, HIS 21, PRO 28, MET 14 (residue and the binding sites it lines).

Found with

  • MG · Magnesium ion
  • ZN · Zinc ion
  • FAD · Flavin-adenine dinucleotide
  • EDO · 1,2-ethanediol
  • CL · Chloride ion
  • FMT · Formic acid
  • 88G · Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide
  • ANP · Phosphoaminophosphonic acid-adenylate ester
  • CDL · Cardiolipin
  • SO4 · Sulfate ion

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