Research workbench

CPAP:TUBULIN:IIH5 alpharep complex

Analyse CPAP:TUBULIN:IIH5 alpharep complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Q1E
Type: protein
Length: 1,230 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha chain; Tubulin beta chain; IIH5 alpharep; Centromere protein J
UniProt: A0A6P7DY20, A0A6P3TCJ9, Q9HC77
Ligands: GTP, MG
Pockets: 18 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha chain	protein	440	45% helix, 17% strand	A0A6P7DY20
B	Tubulin beta chain	protein	433	47% helix, 18% strand	A0A6P3TCJ9
C	IIH5 alpharep	protein	157	77% helix, 0% strand	—
D	IIH5 alpharep	protein	151	74% helix, 0% strand	—
P	Centromere protein J	protein	49	49% helix, 0% strand	Q9HC77

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · chains A, C

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

Pockets

18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	865	0.81	0.83	88	GTP, MG
2	148	0.68	0.89	31	GOL
3	206	0.62	0.82	36	GTP, MG
4	117	0.61	0.87	35	empty
5	60	0.58	0.90	17	empty

Interfaces

5 interfaces between chains.

A–B · 1362 Å² buried · 15 hydrogen bonds · protein-protein
B–P · 1045 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 797 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 742 Å² buried · 10 hydrogen bonds · protein-protein
A–P · 209 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7Q1E · CPAP:TUBULIN:IIH5 alpharep complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9HC77 · AlphaFold monomer V2.0 prediction for centromere protein J (Q9HC77) · a predicted model of the same protein · chain P against A, TM-score 0.51

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 A0A6P7DY20
Every structure of UniProt A0A6P3TCJ9
Every structure of UniProt Q9HC77
Elsewhere: RCSB PDB 7Q1E · PDBe 7Q1E · UniProt A0A6P7DY20 · UniProt A0A6P3TCJ9 · UniProt Q9HC77

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