MolNFT v1 · #174747 · protein

Crystal structure of TRF2 trfh domain in complex with a MCPH1 peptide

7C5D · Telomeric repeat-binding factor 2: “Crystal structure of TRF2 trfh domain in complex with a MCPH1 peptide”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #174747 on GenesisL1: 3D structure, binding sites and…

PDB: 7C5D
Type: protein
Length: 421 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Telomeric repeat-binding factor 2; Microcephalin
UniProt: Q15554, Q8NEM0
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Telomeric repeat-binding factor 2	protein	194	72% helix, 1% strand	Q15554
B	Telomeric repeat-binding factor 2	protein	199	71% helix, 0% strand	Q15554
C	Microcephalin	protein	16	25% helix, 6% strand	Q8NEM0
D	Microcephalin	protein	12	33% helix, 0% strand	Q8NEM0

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains B, D, A

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

Pockets

4 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	800	0.76	0.80	84	empty
2	207	0.61	0.81	23	empty
3	71	0.33	0.75	13	empty
4	55	0.26	0.73	15	GOL

Interfaces

3 interfaces between chains.

A–C · 754 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 731 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 528 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7C5D · Crystal structure of TRF2 TRFH domain in complex with a MCPH1 peptide · the same entry in another collection · chain D against D, TM-score 1.00
Q15554 · AlphaFold monomer V2.0 prediction for telomeric repeat-binding factor 2 (Q15554) · a predicted model of the same protein · chain B against A, TM-score 0.98
Q8NEM0 · AlphaFold monomer V2.0 prediction for microcephalin (Q8NEM0) · a predicted model of the same protein · chain D against A, TM-score 0.49

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 Q15554
Every structure of UniProt Q8NEM0
Elsewhere: RCSB PDB 7C5D · PDBe 7C5D · UniProt Q15554 · UniProt Q8NEM0

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