MolNFT v1 · #71692 · protein

Crystal structure of the thermus thermophilus transcription-repair coupling factor RNA polymerase interacting domain with the thermus aquaticus RNA polymerase BETA1 domain

3MLQ · DNA-directed RNA polymerase subunit beta: “Crystal structure of the thermus thermophilus transcription-repair coupling factor RNA polymerase interacting…”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.73).…

PDB: 3MLQ
Type: protein
Length: 883 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit beta; Transcription-repair coupling factor
EC: 2.7.7.6
UniProt: Q9KWU7, Q72KB4
Ligands: PO4
Pockets: 12 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 34% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	186	40% helix, 25% strand	Q9KWU7
B	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	180	43% helix, 27% strand	Q9KWU7
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	182	39% helix, 26% strand	Q9KWU7
D	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	185	42% helix, 25% strand	Q9KWU7
E	Transcription-repair coupling factor	protein	38	0% helix, 71% strand	Q72KB4
F	Transcription-repair coupling factor	protein	30	0% helix, 60% strand	Q72KB4
G	Transcription-repair coupling factor	protein	40	0% helix, 50% strand	Q72KB4
H	Transcription-repair coupling factor	protein	42	0% helix, 50% strand	Q72KB4

Ligands and binding sites

PO4 · Phosphate ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	756	0.73	0.79	83	empty
2	753	0.69	0.76	78	empty
3	239	0.52	0.76	30	empty
4	147	0.50	0.78	21	empty
5	116	0.45	0.78	23	empty

Interfaces

13 interfaces between chains.

A–B · 782 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 773 Å² buried · 10 hydrogen bonds · protein-protein
D–H · 514 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 481 Å² buried · 8 hydrogen bonds · protein-protein
C–G · 476 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3MLQ · Crystal structure of the Thermus thermophilus transcription-repair coupling factor RNA… · the same entry in another collection · chain H against H, TM-score 1.00
Q9KWU7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q9KWU7) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 Q9KWU7
Every structure of UniProt Q72KB4
Elsewhere: RCSB PDB 3MLQ · PDBe 3MLQ · UniProt Q9KWU7 · UniProt Q72KB4

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