Research workbench

Crystal structure of escherichia COLI RNA polymerase in complex with salinamide a

Analyse Crystal structure of escherichia COLI RNA polymerase in complex with salinamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MEX
Type: protein
Length: 7,095 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
Ligands: 28H, 28K, ZN, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 11 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	298	29% helix, 30% strand	P0A7Z4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	287	27% helix, 30% strand	P0A7Z4
C, I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	32% helix, 23% strand	P0A8V2
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1150	43% helix, 12% strand	P0A8T7
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	89	67% helix, 0% strand	P0A800
F, L	RNA polymerase sigma factor rpod	protein	464	69% helix, 2% strand	P00579
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	216	20% helix, 39% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	215	20% helix, 38% strand	P0A7Z4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1143	44% helix, 12% strand	P0A8T7
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	75	67% helix, 0% strand	P0A800
M, N	Salinamide a	protein	7	43% helix, 0% strand	—

Ligands and binding sites

28H · (2R,3R)-3-hydroxy-2,4-dimethylpentanoic acid · ligand · 2 copies · chains D, M, J, N
28K · (2E)-3-{(2S)-2-[(1R)-1-hydroxyethyl]oxiran-2-yl}prop-2-enoic acid · ligand · 2 copies · chains C, M, I, N
ZN · Zinc ion · metal · 4 copies · chains D, J
MG · Magnesium ion · metal · 2 copies · chains D, J

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	1026	0.84	0.85	117	empty
2	763	0.82	0.85	108	empty
3	1115	0.82	0.83	98	empty
4	542	0.79	0.85	75	empty
5	941	0.79	0.81	95	empty

Interfaces

24 interfaces between chains.

I–J · 7412 Å² buried · 88 hydrogen bonds · protein-protein
C–D · 7264 Å² buried · 79 hydrogen bonds · protein-protein
D–F · 2034 Å² buried · 28 hydrogen bonds · protein-protein
J–L · 2023 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1943 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 6 covalent (nonstandard, covalent ligand).

Compared structures

4MEX · Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A · 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
Elsewhere: RCSB PDB 4MEX · PDBe 4MEX · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.