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Cooperative DNA binding by two rela dimers

Analyse Cooperative DNA binding by two rela dimers in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5U01
Type: protein + DNA
Length: 1,146 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription factor P65; DNA (27-mer)
UniProt: Q04207
Pockets: 10 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Transcription factor P65	protein	273	6% helix, 41% strand	Q04207
F, E	DNA (27-mer)	dna	27	—	—

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1027	0.85	0.86	85	empty
2	1052	0.84	0.85	83	empty
3	241	0.58	0.79	38	empty
4	118	0.55	0.84	19	empty
5	99	0.50	0.82	16	empty

Interfaces

13 interfaces between chains.

F–E · 1206 Å² buried · 99 hydrogen bonds · nucleic-nucleic
A–B · 747 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 743 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 695 Å² buried · 16 hydrogen bonds · protein-nucleic
D–F · 660 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

5U01 · Cooperative DNA binding by two RelA dimers · the same entry in another collection · chain C against C, TM-score 1.00
Q04207 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04207) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q04207
Elsewhere: RCSB PDB 5U01 · PDBe 5U01 · UniProt Q04207

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