MolNFT v1 · #32032 · protein

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin

2BE5 · DNA-directed RNA polymerase alpha chain: “Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin”. X-ray diffraction, 3 ligands (TGT, MG, ZN), 20 pockets (best druggability 0.87).…

PDB: 2BE5
Type: protein
Length: 6,818 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase alpha chain; DNA-directed RNA polymerase beta chain…
EC: 2.7.7.6
UniProt: Q9Z9H6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
Ligands: TGT, MG, ZN
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 36% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, K, L	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6)	protein	229	21% helix, 39% strand	Q9Z9H6
C, M	DNA-directed RNA polymerase beta chain (EC 2.7.7.6)	protein	1119	25% helix, 22% strand	Q8RQE9
D, N	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6)	protein	1392	39% helix, 13% strand	Q8RQE8
E, O	RNA polymerase omega chain	protein	95	46% helix, 3% strand	Q8RQE7
F, P	RNA polymerase sigma factor rpod	protein	345	67% helix, 1% strand	Q5SKW1

Ligands and binding sites

TGT · Tagetitoxin · ligand · 2 copies · chains C, D, M, N
MG · Magnesium ion · metal · 4 copies · chains C, D, N, M
ZN · Zinc ion · metal · 4 copies · chains D, 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	961	0.87	0.88	97	empty
2	873	0.84	0.86	93	empty
3	823	0.84	0.87	82	empty
4	1126	0.84	0.85	89	empty
5	516	0.84	0.90	75	empty

Interfaces

20 interfaces between chains.

C–D · 9289 Å² buried · 114 hydrogen bonds · protein-protein
M–N · 8899 Å² buried · 108 hydrogen bonds · protein-protein
N–P · 4189 Å² buried · 59 hydrogen bonds · protein-protein
D–F · 4011 Å² buried · 66 hydrogen bonds · protein-protein
N–O · 2436 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2BE5 · Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with… · the same entry in another collection · chain P against P, 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 Q9Z9H6
Every structure of UniProt Q8RQE9
Every structure of UniProt Q8RQE8
Every structure of UniProt Q8RQE7
Every structure of UniProt Q5SKW1
Elsewhere: RCSB PDB 2BE5 · PDBe 2BE5 · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1

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