MolNFT v1 · #156083 · protein

Crystal structure of tubulin-inhibitor complex

6LSN · Tubulin alpha-1B chain: “Crystal structure of tubulin-inhibitor complex”. X-ray diffraction, 7 ligands (GTP, GDP, ERR), 20 pockets (best druggability 0.85). MolNFT v1 #156083 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6LSN
Type: protein
Length: 2,200 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands: GTP, GDP, ERR, ACP, MG, CA, CL
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Tubulin alpha-1B chain	protein	440	45% helix, 19% strand	Q2XVP4
B	Tubulin beta chain	protein	424	48% helix, 19% strand	A0A287AGU7
D	Tubulin beta chain	protein	421	50% helix, 20% strand	A0A287AGU7
E	Stathmin-4	protein	124	77% helix, 13% strand	P63042
F	Tubulin tyrosine ligase	protein	351	31% helix, 21% 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
ERR · 2-(1-methylindol-5-yl)-7-(3,4,5-trimethoxyphenyl) pyrazolo[1,5-a]pyrimidine · ligand · chains A, B
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 4 copies · chains A, E, B, C
CL · Chloride ion · ion · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1117	0.85	0.87	108	GTP, MG, ERR
2	895	0.81	0.83	93	GTP, MG
3	742	0.80	0.84	83	GDP, MG
4	161	0.78	0.95	33	empty
5	257	0.77	0.90	33	MG, ACP

Interfaces

9 interfaces between chains.

A–E · 1642 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1406 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1298 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 893 Å² buried · 15 hydrogen bonds · protein-protein
A–F · 873 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6LSN · Crystal structure of tubulin-inhibitor complex · the same entry in another collection · chain C against C, TM-score 1.00
P63042 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63042) · a predicted model of the same protein · chain E against A, TM-score 0.76

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 Q2XVP4
Every structure of UniProt A0A287AGU7
Every structure of UniProt P63042
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 6LSN · PDBe 6LSN · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63042 · UniProt E1BQ43

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