Research workbench

Structure of the human ccan deltact complex

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

PDB: 7PKN
Type: protein
Length: 2,310 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Centromere protein H; Centromere protein I; Centromere protein K; Centromere protein L…
UniProt: Q9H3R5, Q92674, Q9BS16, Q8N0S6, Q9NSP4, Q96H22, Q9BU64, Q6IPU0, Q7L2Z9, Q71F23, Q13352
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 11 distinct chains · 56% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Centromere protein H	protein	139	87% helix, 0% strand	Q9H3R5
I	Centromere protein I	protein	379	65% helix, 0% strand	Q92674
K	Centromere protein K	protein	131	81% helix, 1% strand	Q9BS16
L	Centromere protein L	protein	300	37% helix, 24% strand	Q8N0S6
M	Centromere protein M	protein	172	37% helix, 20% strand	Q9NSP4
N	Centromere protein N	protein	318	36% helix, 24% strand	Q96H22
O	Centromere protein O	protein	210	42% helix, 25% strand	Q9BU64
P	Centromere protein P	protein	224	40% helix, 35% strand	Q6IPU0
Q	Centromere protein Q	protein	191	76% helix, 0% strand	Q7L2Z9
U	Centromere protein U	protein	166	87% helix, 0% strand	Q71F23
R	Centromere protein R	protein	80	75% helix, 0% strand	Q13352

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	1194	0.87	0.88	110	empty
2	1138	0.84	0.85	102	empty
3	691	0.83	0.87	73	empty
4	870	0.80	0.82	73	empty
5	153	0.80	0.95	22	empty

Interfaces

24 interfaces between chains.

H–K · 3625 Å² buried · 16 hydrogen bonds · protein-protein
Q–U · 3010 Å² buried · 8 hydrogen bonds · protein-protein
H–I · 2483 Å² buried · 11 hydrogen bonds · protein-protein
P–U · 1769 Å² buried · 10 hydrogen bonds · protein-protein
O–P · 1549 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7PKN · Structure of the human CCAN deltaCT complex · the same entry in another collection · chain R against R, TM-score 1.00
Q9NSP4 · AlphaFold monomer V2.0 prediction for centromere protein M (Q9NSP4) · a predicted model of the same protein · chain M against A, TM-score 0.97

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 Q9H3R5
Every structure of UniProt Q92674
Every structure of UniProt Q9BS16
Every structure of UniProt Q8N0S6
Every structure of UniProt Q9NSP4
Every structure of UniProt Q96H22
Every structure of UniProt Q9BU64
Every structure of UniProt Q6IPU0
Every structure of UniProt Q7L2Z9
Every structure of UniProt Q71F23
Every structure of UniProt Q13352
Elsewhere: RCSB PDB 7PKN · PDBe 7PKN · UniProt Q9H3R5 · UniProt Q92674 · UniProt Q9BS16 · UniProt Q8N0S6 · UniProt Q9NSP4 · UniProt Q96H22 · UniProt Q9BU64 · UniProt Q6IPU0 · UniProt Q7L2Z9 · UniProt Q71F23 · UniProt Q13352

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