MolNFT v1 · #92664 · protein + DNA

RAP1/DNA complex

4GFB · DNA-binding protein RAP1: “RAP1/DNA complex”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.52). MolNFT v1 #92664 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GFB
Type: protein + DNA
Length: 278 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-binding protein RAP1; Telomeric DNA
UniProt: P11938
Ligands: CA
Pockets: 6 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-binding protein RAP1	protein	218	44% helix, 5% strand	P11938
C	Telomeric DNA	dna	29	—	—
D	Telomeric DNA	dna	31	—	—

Ligands and binding sites

CA · Calcium ion · metal · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	120	0.52	0.81	22	empty
2	182	0.52	0.78	23	empty
3	134	0.46	0.78	15	empty
4	81	0.40	0.78	21	empty
5	107	0.37	0.75	12	empty

Interfaces

3 interfaces between chains.

C–D · 1340 Å² buried · 115 hydrogen bonds · nucleic-nucleic
A–C · 1319 Å² buried · 41 hydrogen bonds · protein-nucleic
A–D · 1284 Å² buried · 31 hydrogen bonds · protein-nucleic

Compared structures

4GFB · Rap1/DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
P11938 · AlphaFold monomer V2.0 prediction for DNA-binding protein RAP1 (P11938) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P11938
Elsewhere: RCSB PDB 4GFB · PDBe 4GFB · UniProt P11938

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