SMTL ID : 5uhc.1

Crystal structure of Mycobacterium tuberculosis transcription initiation complex containing 3nt RNA in complex with Rifampin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

hetero-2-1-1-1-1-mer

Ligands

1 x G- G- A: RNA (5'-R(*GP*GP*A)-3')(Non-covalent)

G-G-A.1: 17 residues within 4Å: Chain C: R.613, Q.614, K.884, K.892, H.1034, H.1035, K.1040 Chain D: R.500, D.537, G.538, D.539 Chain H: T.11, C.12, C.13, A.14 Ligands: RFP.2, MG.5 Protein-ligand interaction information (PLIP) not available

1 x RFP: RIFAMPICIN(Non-covalent)

RFP.2: 23 residues within 4Å: Chain C: S.434, Q.435, L.436, S.437, Q.438, F.439, D.441, H.451, R.454, S.456, L.458, R.465, P.489, N.493, I.497, R.613, H.680 Chain F: G.428, D.429, E.430 Chain H: A.14 Ligands: G-G-A.1, G-G-A.1 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:L.436, C:L.458, C:P.489, C:I.497, F:D.429 Hydrogen bonds: C:Q.438, C:F.439, C:F.439, C:R.454, C:S.456, C:S.456, C:R.465, C:N.493 Salt bridges: F:E.430

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain D: C.891, C.968, C.975, C.978 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.891, D:C.968, D:C.975, D:C.978 ZN.4: 5 residues within 4Å: Chain D: C.60, C.62, K.64, C.75, C.78 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.60, D:C.62, D:C.75, D:C.78

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain D: D.535, D.537, D.539 Ligands: G-G-A.1 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.535, D:D.537, D:D.539

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, W. et al., Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition. Mol. Cell (2017)

Release Date

2017-04-12

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma factor SigA: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor SigA

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