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Structure of inner kinetochore ccan complex with MASK1

Analyse Structure of inner kinetochore ccan complex with MASK1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QLF
Type: protein
Length: 1,783 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inner kinetochore subunit IML3; Inner kinetochore subunit CHL4; Inner kinetochore subunit…
UniProt: P38265, P38907, Q06675, Q02732, P53298, P38313, Q12493, Q06162
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 8 distinct chains · 50% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Inner kinetochore subunit IML3	protein	241	28% helix, 23% strand	P38265
N	Inner kinetochore subunit CHL4	protein	371	35% helix, 19% strand	P38907
O	Inner kinetochore subunit MCM21	protein	205	36% helix, 27% strand	Q06675
P	Inner kinetochore subunit CTF19	protein	228	33% helix, 27% strand	Q02732
Q	Inner kinetochore subunit OKP1	protein	204	72% helix, 0% strand	P53298
U	Inner kinetochore subunit AME1	protein	171	81% helix, 0% strand	P38313
Y	Inner kinetochore subunit NKP1	protein	223	69% helix, 1% strand	Q12493
Z	Inner kinetochore subunit NKP2	protein	140	73% helix, 0% strand	Q06162

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1047	0.83	0.84	113	empty
2	1061	0.82	0.83	101	empty
3	502	0.76	0.84	63	empty
4	982	0.76	0.78	111	empty
5	446	0.63	0.77	46	empty

Interfaces

19 interfaces between chains.

Y–Z · 3372 Å² buried · 8 hydrogen bonds · protein-protein
Q–U · 3026 Å² buried · 15 hydrogen bonds · protein-protein
O–P · 2318 Å² buried · 18 hydrogen bonds · protein-protein
N–O · 2065 Å² buried · 16 hydrogen bonds · protein-protein
Q–Y · 1853 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6QLF · Structure of inner kinetochore CCAN complex with mask1 · the same entry in another collection · chain Z against Z, TM-score 1.00
Q06675 · AlphaFold monomer V2.0 prediction for inner kinetochore subunit MCM21 (Q06675) · a predicted model of the same protein · chain O against A, TM-score 0.98
Q02732 · AlphaFold monomer V2.0 prediction for inner kinetochore subunit CTF19 (Q02732) · a predicted model of the same protein · chain P against A, TM-score 0.98
P38265 · AlphaFold monomer V2.0 prediction for inner kinetochore subunit IML3 (P38265) · a predicted model of the same protein · chain L against A, TM-score 0.96
P38313 · AlphaFold monomer V2.0 prediction for inner kinetochore subunit AME1 (P38313) · a predicted model of the same protein · chain U against A, TM-score 0.70

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 P38265
Every structure of UniProt P38907
Every structure of UniProt Q06675
Every structure of UniProt Q02732
Every structure of UniProt P53298
Every structure of UniProt P38313
Every structure of UniProt Q12493
Every structure of UniProt Q06162
Elsewhere: RCSB PDB 6QLF · PDBe 6QLF · UniProt P38265 · UniProt P38907 · UniProt Q06675 · UniProt Q02732 · UniProt P53298 · UniProt P38313 · UniProt Q12493 · UniProt Q06162

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