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Crystal structure of a mycobacterium smegmatis transcription initiation complex with rifampicin-resistant RNA polymerase and bound to kanglemycin a

Analyse Crystal structure of a mycobacterium smegmatis transcription initiation complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DCF
Type: protein + DNA
Length: 2,999 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA polymerase-binding protein rbpa; DNA-directed RNA polymerase subunit alpha…
EC: 2.7.7.6
UniProt: A0QZ11, A0QSL8, P60281, A0QS66, A0QWT1, A0QW02
Ligands: KNG, GLU, ZN, MG, SO4
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 9 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
J	RNA polymerase-binding protein rbpa	protein	85	28% helix, 21% strand	A0QZ11
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	219	18% helix, 38% strand	A0QSL8
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	225	19% helix, 36% strand	A0QSL8
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	858	24% helix, 23% strand	P60281
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1176	44% helix, 14% strand	A0QS66
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	82	46% helix, 5% strand	A0QWT1
F	RNA polymerase sigma factor siga	protein	297	70% helix, 1% strand	A0QW02
O	DNA (31-mer)	dna	31	—	—
P	DNA (26-mer)	dna	26	—	—

Ligands and binding sites

KNG · Kanglemycin A · ligand · chains C
GLU · Glutamic acid · ligand · chains D
ZN · Zinc ion · metal · 2 copies · chains D
MG · Magnesium ion · metal · chains D
SO4 · Sulfate ion · ion · 9 copies · chains B, C, D, F
EDO · 1,2-ethanediol · additive · 2 copies · chains D, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	793	0.85	0.87	72	empty
2	511	0.79	0.86	67	SO4
3	212	0.79	0.92	43	empty
4	1037	0.76	0.78	96	SO4
5	384	0.74	0.84	33	empty

Interfaces

18 interfaces between chains.

C–D · 6516 Å² buried · 74 hydrogen bonds · protein-protein
D–F · 2354 Å² buried · 34 hydrogen bonds · protein-protein
D–E · 2065 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 2034 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1703 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6DCF · Crystal structure of a Mycobacterium smegmatis transcription initiation complex with… · the same entry in another collection · chain P against P, TM-score 1.00
P60281 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P60281) · a predicted model of the same protein · chain C against A, TM-score 0.98
A0QS66 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (A0QS66) · a predicted model of the same protein · chain D against A, TM-score 0.97
A0QSL8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (A0QSL8) · a predicted model of the same protein · chain A against A, TM-score 0.94

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0QZ11
Every structure of UniProt A0QSL8
Every structure of UniProt P60281
Every structure of UniProt A0QS66
Every structure of UniProt A0QWT1
Every structure of UniProt A0QW02
Elsewhere: RCSB PDB 6DCF · PDBe 6DCF · UniProt A0QZ11 · UniProt A0QSL8 · UniProt P60281 · UniProt A0QS66 · UniProt A0QWT1 · UniProt A0QW02

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