MolNFT v1 · #68785 · protein

Crystal structure of RAP1 and TRF2 complex

3K6G · Telomeric repeat-binding factor 2-interacting protein 1: “Crystal structure of RAP1 and TRF2 complex”. X-ray diffraction, 3 pockets (best druggability 0.65). MolNFT v1 #68785 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3K6G
Type: protein
Length: 380 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Telomeric repeat-binding factor 2-interacting protein 1; Telomeric repeat-binding factor 2
UniProt: Q9NYB0, Q15554
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 5 distinct chains · 69% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Telomeric repeat-binding factor 2-interacting protein 1	protein	93	71% helix, 0% strand	Q9NYB0
B	Telomeric repeat-binding factor 2-interacting protein 1	protein	92	74% helix, 1% strand	Q9NYB0
D	Telomeric repeat-binding factor 2	protein	33	67% helix, 0% strand	Q15554
E	Telomeric repeat-binding factor 2	protein	36	58% helix, 3% strand	Q15554
F	Telomeric repeat-binding factor 2	protein	33	64% helix, 3% strand	Q15554

Pockets

3 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	485	0.65	0.77	44	empty
2	233	0.56	0.78	24	empty
3	210	0.53	0.78	27	empty

Interfaces

10 interfaces between chains.

B–E · 1193 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 1109 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 1088 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 184 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 155 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (engineered).

Compared structures

3K6G · Crystal structure of Rap1 and TRF2 complex · the same entry in another collection · chain F against F, TM-score 1.00
Q9NYB0 · AlphaFold monomer V2.0 prediction for telomeric repeat-binding factor 2-interacting… · a predicted model of the same protein · chain A against A, TM-score 0.99
Q15554 · AlphaFold monomer V2.0 prediction for telomeric repeat-binding factor 2 (Q15554) · a predicted model of the same protein · chain F against A, TM-score 0.86

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 Q9NYB0
Every structure of UniProt Q15554
Elsewhere: RCSB PDB 3K6G · PDBe 3K6G · UniProt Q9NYB0 · UniProt Q15554

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