MolNFT v1 · #185198 · protein

Inhibiting parasite proliferation using a rationally designed anti- tubulin agent

7PJF · Tubulin alpha-1B chain: “Inhibiting parasite proliferation using a rationally designed anti- tubulin agent”. X-ray diffraction, 2 ligands (GTP, MG), 11 pockets (best druggability 0.77). MolNFT v1 #185198 on GenesisL1: 3D structure…

PDB: 7PJF
Type: protein
Length: 1,002 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta-3 chain; Designed ankyrin repeat protein (darpin) D1
UniProt: P68363, Q13509
Ligands: GTP, MG
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	419	47% helix, 18% strand	P68363
B	Tubulin beta-3 chain	protein	428	48% helix, 18% strand	Q13509
F	Designed ankyrin repeat protein (darpin) D1	protein	155	54% helix, 0% strand	—

Ligands and binding sites

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

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	409	0.77	0.87	53	GTP, MG
2	522	0.66	0.77	55	empty
3	338	0.60	0.77	44	empty
4	183	0.59	0.82	30	empty
5	200	0.59	0.81	35	GTP, MG

Interfaces

2 interfaces between chains.

A–B · 1374 Å² buried · 13 hydrogen bonds · protein-protein
B–F · 873 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7PJF · Inhibiting parasite proliferation using a rationally designed anti-tubulin agent · the same entry in another collection · chain A against A, TM-score 1.00
Q13509 · AlphaFold monomer V2.0 prediction for tubulin beta-3 chain (Q13509) · a predicted model of the same protein · chain B against A, TM-score 0.98
P68363 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P68363) · a predicted model of the same protein · chain A 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 P68363
Every structure of UniProt Q13509
Elsewhere: RCSB PDB 7PJF · PDBe 7PJF · UniProt P68363 · UniProt Q13509

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