MolNFT v1 · #145042 · protein + DNA

Crystal structure of a mycobacterium smegmatis RNA polymerase transcription initiation complex with inhibitor kanglemycin a

6CCE · RNA polymerase-binding protein rbpa: “Crystal structure of a mycobacterium smegmatis RNA polymerase transcription initiation complex with inhibitor…”. X-ray diffraction, 5 ligands (KNG, GLU, ZN), 20 pockets (best druggability 0.83).…

PDB: 6CCE
Type: protein + DNA
Length: 3,228 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 0.83

Structure

x-ray diffraction · 9 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
J	RNA polymerase-binding protein rbpa	protein	36	78% helix, 0% strand	A0QZ11
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	221	18% helix, 40% strand	A0QSL8
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	226	20% helix, 38% strand	A0QSL8
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1095	26% helix, 26% strand	P60281
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1195	46% helix, 14% strand	A0QS66
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	77	48% helix, 5% strand	A0QWT1
F	RNA polymerase sigma factor siga	protein	302	73% helix, 2% strand	A0QW02
O	DNA (57-mer)	dna	57	—	—
G	POLY(UNK)	protein	19	79% helix, 0% strand	—

Ligands and binding sites

KNG · Kanglemycin A · ligand · chains C, F
GLU · Glutamic acid · ligand · chains D
ZN · Zinc ion · metal · chains D
MG · Magnesium ion · metal · chains D
SO4 · Sulfate ion · ion · 8 copies · chains C, B, D, F
EDO · 1,2-ethanediol · additive · 3 copies · chains F, O, D

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	1038	0.83	0.84	103	SO4
2	253	0.79	0.91	50	empty
3	583	0.78	0.84	89	empty
4	578	0.77	0.84	68	SO4
5	570	0.76	0.83	61	empty

Interfaces

17 interfaces between chains.

C–D · 8016 Å² buried · 105 hydrogen bonds · protein-protein
D–F · 2319 Å² buried · 35 hydrogen bonds · protein-protein
D–E · 2121 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 2080 Å² buried · 7 hydrogen bonds · protein-protein
F–O · 2020 Å² buried · 47 hydrogen bonds · protein-nucleic

Compared structures

6CCE · Crystal structure of a Mycobacterium smegmatis RNA polymerase transcription initiation… · the same entry in another collection · chain O against O, 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 0.99
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 0.98
A0QWT1 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (A0QWT1) · a predicted model of the same protein · chain E against A, TM-score 0.95

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 6CCE · PDBe 6CCE · UniProt A0QZ11 · UniProt A0QSL8 · UniProt P60281 · UniProt A0QS66 · UniProt A0QWT1 · UniProt A0QW02

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