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Structure of a mycobacterium smegmatis transcription initiation complex with an upstream-fork promoter fragment

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

PDB: 5VI8
Type: protein + DNA
Length: 3,386 residues
Chains: 10
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: ZN, MG, SO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 10 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
J	RNA polymerase-binding protein rbpa	protein	83	27% helix, 23% strand	A0QZ11
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	218	19% helix, 39% strand	A0QSL8
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	233	19% helix, 37% strand	A0QSL8
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1099	27% helix, 25% strand	P60281
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1248	47% helix, 14% strand	A0QS66
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	76	47% helix, 5% strand	A0QWT1
F	RNA polymerase sigma factor siga	protein	319	71% helix, 2% strand	A0QW02
O	DNA (31-mer)	dna	31	—	—
P	DNA (26-mer)	dna	26	—	—
T	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	53	68% helix, 0% strand	A0QSL8

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains D
MG · Magnesium ion · metal · chains D
SO4 · Sulfate ion · ion · 12 copies · chains C, D, F, O
EDO · 1,2-ethanediol · additive · 6 copies · chains C, 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	798	0.80	0.83	86	empty
2	661	0.78	0.83	81	empty
3	719	0.78	0.83	93	EDO
4	402	0.75	0.85	34	empty
5	959	0.74	0.77	80	SO4

Interfaces

22 interfaces between chains.

C–D · 7965 Å² buried · 100 hydrogen bonds · protein-protein
D–F · 2483 Å² buried · 29 hydrogen bonds · protein-protein
C–F · 2368 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 2141 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 2039 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

5VI8 · Structure of a mycobacterium smegmatis transcription initiation complex with an… · the same entry in another collection · chain T against T, 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

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 5VI8 · PDBe 5VI8 · UniProt A0QZ11 · UniProt A0QSL8 · UniProt P60281 · UniProt A0QS66 · UniProt A0QWT1 · UniProt A0QW02

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