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Structure of inner kinetochore ccan complex

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

PDB: 6QLE
Type: protein
Length: 2,415 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Central kinetochore subunit MCM16,CENTRAL kinetochore subunit MCM16,INNER kinetochore…
UniProt: B3LLA4, Q12748, P47167, P38265, P38907, Q06675, Q02732, P53298, P38313, Q12493, Q06162
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 11 distinct chains · 55% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Central kinetochore subunit MCM16,CENTRAL kinetochore subunit MCM16,INNER kinetochore subunit MCM16,MCM16P	protein	126	85% helix, 0% strand	B3LLA4
I	Central kinetochore subunit CTF3,INNER kinetochore subunit CTF3,CENTRAL kinetochore subunit CTF3,INNER kinetochore subunit CTF3	protein	365	62% helix, 0% strand	Q12748
K	Inner kinetochore subunit MCM22,INNER kinetochore subunit MCM22,INNER kinetochore subunit MCM22,INNER kinetochore subunit MCM22	protein	106	91% helix, 0% strand	P47167
L	Inner kinetochore subunit IML3	protein	241	27% helix, 19% strand	P38265
N	Inner kinetochore subunit CHL4	protein	371	33% helix, 19% strand	P38907
O	Inner kinetochore subunit MCM21	protein	205	36% helix, 27% strand	Q06675
P	Inner kinetochore subunit CTF19	protein	242	33% helix, 26% strand	Q02732
Q	Inner kinetochore subunit OKP1,INNER kinetochore subunit OKP1,INNER kinetochore subunit OKP1,INNER kinetochore subunit OKP1	protein	224	70% helix, 0% strand	P53298
U	Inner kinetochore subunit AME1,INNER kinetochore subunit AME1,INNER kinetochore subunit AME1,INNER kinetochore subunit AME1	protein	172	83% helix, 0% strand	P38313
Y	Inner kinetochore subunit NKP1	protein	223	70% helix, 0% strand	Q12493
Z	Inner kinetochore subunit NKP2	protein	140	79% helix, 0% strand	Q06162

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	961	0.83	0.84	105	empty
2	1198	0.81	0.83	110	empty
3	638	0.78	0.83	79	empty
4	620	0.78	0.83	82	empty
5	209	0.71	0.87	34	empty

Interfaces

26 interfaces between chains.

Y–Z · 3386 Å² buried · 8 hydrogen bonds · protein-protein
Q–U · 3253 Å² buried · 14 hydrogen bonds · protein-protein
H–K · 2835 Å² buried · 7 hydrogen bonds · protein-protein
H–I · 2438 Å² buried · 15 hydrogen bonds · protein-protein
O–P · 2335 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6QLE · Structure of inner kinetochore CCAN complex · 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

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 B3LLA4
Every structure of UniProt Q12748
Every structure of UniProt P47167
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 6QLE · PDBe 6QLE · UniProt B3LLA4 · UniProt Q12748 · UniProt P47167 · UniProt P38265 · UniProt P38907 · UniProt Q06675 · UniProt Q02732 · UniProt P53298 · UniProt P38313 · UniProt Q12493 · UniProt Q06162

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