MolNFT v1 · #118319 · protein + DNA

X-ray structure of REB1-ter complex

5EYB · DNA-binding protein REB1: “X-ray structure of REB1-ter complex”. X-ray diffraction, 15 pockets (best druggability 0.80). MolNFT v1 #118319 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EYB
Type: protein + DNA
Length: 781 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-binding protein REB1; DNA (26-mer)
UniProt: Q9P6H9
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-binding protein REB1	protein	340	65% helix, 0% strand	Q9P6H9
C, E	DNA (26-mer)	dna	26	—	—
D, F	DNA (26-mer)	dna	26	—	—
B	DNA-binding protein REB1	protein	337	65% helix, 0% strand	Q9P6H9

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.80	0.98	16	empty
2	93	0.77	0.98	15	empty
3	948	0.76	0.79	71	empty
4	1043	0.74	0.77	91	empty
5	287	0.55	0.76	35	empty

Interfaces

8 interfaces between chains.

A–C · 1268 Å² buried · 29 hydrogen bonds · protein-nucleic
B–E · 1234 Å² buried · 30 hydrogen bonds · protein-nucleic
A–D · 1160 Å² buried · 10 hydrogen bonds · protein-nucleic
C–D · 1124 Å² buried · 91 hydrogen bonds · nucleic-nucleic
E–F · 1118 Å² buried · 93 hydrogen bonds · nucleic-nucleic

Compared structures

5EYB · X-ray Structure of Reb1-Ter Complex · the same entry in another collection · chain F against F, TM-score 1.00
Q9P6H9 · AlphaFold monomer V2.0 prediction for DNA-binding protein REB1 (Q9P6H9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9P6H9
Elsewhere: RCSB PDB 5EYB · PDBe 5EYB · UniProt Q9P6H9

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