Research workbench

X-ray crystal structure of escherichia COLI RNA polymerase and trar complex

Analyse X-ray crystal structure of escherichia COLI RNA polymerase and trar complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W1S
Type: protein
Length: 7,224 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6
UniProt: P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579, P41065
Ligands: ZN, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 13 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	319	27% helix, 27% strand	P0A7Z4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	217	17% helix, 30% strand	P0A7Z4
C, I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	30% helix, 23% strand	P0A8V2
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1173	42% helix, 14% strand	P0A8T7
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	89	62% helix, 0% strand	P0A800
F	RNA polymerase sigma factor rpod	protein	468	64% helix, 3% strand	P00579
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	227	20% helix, 38% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	216	18% helix, 36% strand	P0A7Z4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1155	43% helix, 14% strand	P0A8T7
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	72	60% helix, 0% strand	P0A800
L	RNA polymerase sigma factor rpod	protein	469	65% helix, 3% strand	P00579
M	Protein trar	protein	70	57% helix, 3% strand	P41065
N	Protein trar	protein	69	57% helix, 3% strand	P41065

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains D, J, M, N
MG · Magnesium ion · metal · 2 copies · chains D, M, J, N

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	625	0.83	0.87	66	empty
2	564	0.83	0.88	58	empty
3	632	0.82	0.87	71	empty
4	1169	0.82	0.83	112	empty
5	266	0.80	0.92	42	empty

Interfaces

26 interfaces between chains.

C–D · 8303 Å² buried · 98 hydrogen bonds · protein-protein
I–J · 8296 Å² buried · 102 hydrogen bonds · protein-protein
D–F · 2798 Å² buried · 32 hydrogen bonds · protein-protein
J–L · 2753 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2145 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5W1S · X-ray crystal structure of Escherichia coli RNA polymerase and TraR complex · the same entry in another collection · chain N against N, TM-score 1.00

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 P0A7Z4
Every structure of UniProt P0A8V2
Every structure of UniProt P0A8T7
Every structure of UniProt P0A800
Every structure of UniProt P00579
Every structure of UniProt P41065
Elsewhere: RCSB PDB 5W1S · PDBe 5W1S · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt P41065

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