MolNFT v1 · #85059 · protein + DNA

Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex

4A0L · DNA damage-binding protein 1: “Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #85059 on GenesisL1: 3D structure, binding sites…

PDB: 4A0L
Type: protein + DNA
Length: 4,428 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA damage-binding protein 1; DNA damage-binding protein 2; Cullin-4B; E3…
UniProt: Q16531, Q2YDS1, Q13620, P62878
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 23% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DNA damage-binding protein 1	protein	1105	6% helix, 49% strand	Q16531
B, D	DNA damage-binding protein 2	protein	355	7% helix, 45% strand	Q2YDS1
E, H	Cullin-4B	protein	709	57% helix, 7% strand	Q13620
F, I	E3 ubiquitin-protein ligase RBX1	protein	21	0% helix, 52% strand	P62878
R, T	12 bp thf containing DNA duplex	dna	12	—	—
S, U	12 bp DNA duplex	dna	12	—	—

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	1135	0.86	0.87	112	empty
2	525	0.85	0.92	73	empty
3	958	0.80	0.82	83	empty
4	840	0.79	0.82	74	empty
5	312	0.78	0.89	52	empty

Interfaces

12 interfaces between chains.

C–D · 2158 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2063 Å² buried · 17 hydrogen bonds · protein-protein
C–H · 1871 Å² buried · 19 hydrogen bonds · protein-protein
H–I · 1753 Å² buried · 28 hydrogen bonds · protein-protein
E–F · 1626 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

4A0L · Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex · the same entry in another collection · chain U against U, 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 Q16531
Every structure of UniProt Q2YDS1
Every structure of UniProt Q13620
Every structure of UniProt P62878
Elsewhere: RCSB PDB 4A0L · PDBe 4A0L · UniProt Q16531 · UniProt Q2YDS1 · UniProt Q13620 · UniProt P62878

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