MolNFT v1 · #125042 · protein

Crystal structure of tubulin-stathmin-ttl-compound 11 complex

5KX5 · Tubulin alpha chain: “Crystal structure of tubulin-stathmin-ttl-compound 11 complex”. X-ray diffraction, 6 ligands (GTP, GDP, 6YK), 20 pockets (best druggability 0.83). MolNFT v1 #125042 on GenesisL1: 3D structure, binding sites and…

PDB: 5KX5
Type: protein
Length: 2,193 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha chain; Tubulin beta chain; Stathmin-4; Ttl protein
UniProt: D0VWZ0, D0VWY9, P63043, E1BQ43
Ligands: GTP, GDP, 6YK, ADP, MG, CA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha chain	protein	441	43% helix, 18% strand	D0VWZ0
B	Tubulin beta chain	protein	427	48% helix, 19% strand	D0VWY9
C	Tubulin alpha chain	protein	440	46% helix, 17% strand	D0VWZ0
D	Tubulin beta chain	protein	426	49% helix, 19% strand	D0VWY9
E	Stathmin-4	protein	121	76% helix, 12% strand	P63043
F	Ttl protein	protein	338	29% helix, 22% strand	E1BQ43

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
6YK · (2~{S},4~{R})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-3-[[(2~{S},3~{S})-2-[[(2~{R})-1,2-dimethylpyrrolidin-2-yl]carbonylamino]-3-methyl-pentanoyl]-methyl-amino]-4-methyl-pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-(4-aminophenyl)-2-methyl-pentanoic acid · ligand · 2 copies · chains B, C, D
ADP · Adenosine-5'-diphosphate · ligand · chains F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, E

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	214	0.83	0.96	46	empty
2	1136	0.81	0.83	113	GDP, MG, 6YK
3	479	0.79	0.87	58	GTP, MG
4	404	0.78	0.87	51	GTP, MG
5	1035	0.75	0.78	72	empty

Interfaces

9 interfaces between chains.

A–E · 1739 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1446 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1445 Å² buried · 18 hydrogen bonds · protein-protein
A–F · 1110 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 939 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5KX5 · Crystal structure of tubulin-stathmin-TTL-Compound 11 complex · the same entry in another collection · chain A against A, TM-score 1.00

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 D0VWZ0
Every structure of UniProt D0VWY9
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 5KX5 · PDBe 5KX5 · UniProt D0VWZ0 · UniProt D0VWY9 · UniProt P63043 · UniProt E1BQ43

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