MolNFT v1 · #139011 · protein + DNA + RNA

Crystal structure of thermus thermophilus transcription initiation complex with gpa and cmpcpp

5X22 · DNA-directed RNA polymerase subunit alpha: “Crystal structure of thermus thermophilus transcription initiation complex with gpa and cmpcpp”. X-ray diffraction, 3 ligands (2TM, MG, ZN), 20 pockets (best druggability 0.87). MolNFT v1…

PDB: 5X22
Type: protein + DNA + RNA
Length: 7,028 residues
Chains: 18
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: Q9Z9H6, Q8RQE9, Q8RQE8, Q72ID6, Q72L95
Ligands: 2TM, MG, ZN
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 13 distinct chains · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, K	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	231	22% helix, 42% strand	Q9Z9H6
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	223	22% helix, 41% strand	Q9Z9H6
C, M	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1112	29% helix, 27% strand	Q8RQE9
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1438	34% helix, 24% strand	Q8RQE8
E, O	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	94	49% helix, 11% strand	Q72ID6
F	RNA polymerase sigma factor siga	protein	327	68% helix, 2% strand	Q72L95
G, Q	Promoter DNA template strand	dna	19	—	—
H	Promoter DNA nontemplate strand	dna	27	—	—
I, S	RNA (5'-R(GPA)-3')	rna	2	—	—
L	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	227	21% helix, 41% strand	Q9Z9H6
N	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1500	37% helix, 24% strand	Q8RQE8
P	RNA polymerase sigma factor siga	protein	346	70% helix, 2% strand	Q72L95
R	Promoter DNA nontemplate strand	dna	24	—	—

Ligands and binding sites

2TM · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · 2 copies · chains C, D, G, I, M, N, Q, S
MG · Magnesium ion · metal · 12 copies · chains B, D, I, F, L, N, S, M, P
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	1179	0.87	0.89	137	empty
2	1094	0.87	0.88	111	empty
3	995	0.86	0.87	90	empty
4	1014	0.86	0.87	92	empty
5	1089	0.86	0.86	99	empty

Interfaces

43 interfaces between chains.

M–N · 9132 Å² buried · 125 hydrogen bonds · protein-protein
C–D · 9070 Å² buried · 120 hydrogen bonds · protein-protein
D–F · 4156 Å² buried · 47 hydrogen bonds · protein-protein
N–P · 4058 Å² buried · 51 hydrogen bonds · protein-protein
C–F · 2506 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5X22 · Crystal structure of Thermus thermophilus transcription initiation complex with GpA and… · the same entry in another collection · chain R against R, 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 Q72ID6
Every structure of UniProt Q72L95
Elsewhere: RCSB PDB 5X22 · PDBe 5X22 · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q72ID6 · UniProt Q72L95

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