Research workbench

Drosophila GDP-tubulin

Analyse Drosophila GDP-tubulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TIS
Type: protein
Length: 1,850 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1 chain; Tubulin beta-1 chain; Stathmin-4
UniProt: P06603, Q24560, P63043
Ligands: GTP, GDP, MG, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1 chain	protein	433	46% helix, 18% strand	P06603
B	Tubulin beta-1 chain	protein	430	50% helix, 19% strand	Q24560
C	Tubulin alpha-1 chain	protein	428	46% helix, 18% strand	P06603
D	Tubulin beta-1 chain	protein	429	50% helix, 19% strand	Q24560
E	Stathmin-4	protein	130	71% helix, 13% strand	P63043

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, E, B, C

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

Pockets

20 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	1068	0.83	0.84	126	GDP, GOL
2	1037	0.81	0.82	101	GTP, MG, SO4
3	456	0.76	0.85	60	GTP, MG
4	522	0.69	0.79	51	empty
5	362	0.67	0.81	29	empty

Interfaces

7 interfaces between chains.

A–E · 1714 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 1454 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1401 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1378 Å² buried · 23 hydrogen bonds · protein-protein
C–E · 824 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

P06603 · AlphaFold monomer V2.0 prediction for tubulin alpha-1 chain (P06603) · a predicted model of the same protein · chain C against A, TM-score 0.98
Q24560 · AlphaFold monomer V2.0 prediction for tubulin beta-1 chain (Q24560) · a predicted model of the same protein · chain B 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 P06603
Every structure of UniProt Q24560
Every structure of UniProt P63043
Elsewhere: RCSB PDB 6TIS · PDBe 6TIS · UniProt P06603 · UniProt Q24560 · UniProt P63043

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