MolNFT v1 · #179494 · protein

CBF3

7K79 · Centromere DNA-binding protein complex CBF3 subunit C: “CBF3”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #179494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K79
Type: protein
Length: 1,601 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Centromere DNA-binding protein complex CBF3 subunit C; Centromere DNA-binding protein…
UniProt: P35203, P40969, P52286
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 4 distinct chains · 49% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	Centromere DNA-binding protein complex CBF3 subunit C	protein	408	25% helix, 12% strand	P35203
L	Centromere DNA-binding protein complex CBF3 subunit B	protein	525	60% helix, 1% strand	P40969
O	Centromere DNA-binding protein complex CBF3 subunit B	protein	517	59% helix, 1% strand	P40969
N	Suppressor of kinetochore protein 1	protein	151	38% helix, 2% strand	P52286

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	1114	0.89	0.90	156	empty
2	762	0.82	0.85	88	empty
3	113	0.75	0.94	19	empty
4	101	0.75	0.95	22	empty
5	299	0.74	0.87	39	empty

Interfaces

4 interfaces between chains.

L–O · 2960 Å² buried · 36 hydrogen bonds · protein-protein
K–N · 2193 Å² buried · 22 hydrogen bonds · protein-protein
K–L · 1384 Å² buried · 9 hydrogen bonds · protein-protein
L–N · 854 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7K79 · CBF3 · the same entry in another collection · chain N against N, TM-score 1.00
P40969 · AlphaFold monomer V2.0 prediction for centromere DNA-binding protein complex CBF3 subunit… · a predicted model of the same protein · chain O against A, TM-score 0.97
P35203 · AlphaFold monomer V2.0 prediction for centromere DNA-binding protein complex CBF3 subunit… · a predicted model of the same protein · chain K against A, TM-score 0.91
P52286 · AlphaFold monomer V2.0 prediction for suppressor of kinetochore protein 1 (P52286) · a predicted model of the same protein · chain N against A, TM-score 0.80

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 P35203
Every structure of UniProt P40969
Every structure of UniProt P52286
Elsewhere: RCSB PDB 7K79 · PDBe 7K79 · UniProt P35203 · UniProt P40969 · UniProt P52286

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