MolNFT v1 · #115115 · protein

Crystal structure of T2R-ttl-lexibulin complex

5CA0 · Tubulin alpha-1B chain: “Crystal structure of T2R-ttl-lexibulin complex”. X-ray diffraction, 6 ligands (GTP, GDP, LXL), 20 pockets (best druggability 0.85). MolNFT v1 #115115 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5CA0
Type: protein
Length: 2,179 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Uncharacterized protein; Stathmin-4
UniProt: Q2XVP4, F2Z5B2, P63043, E1BQ43
Ligands: GTP, GDP, LXL, ACP, MG, CA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	437	46% helix, 19% strand	Q2XVP4
B	Uncharacterized protein	protein	426	46% helix, 19% strand	F2Z5B2
C	Tubulin alpha-1B chain	protein	440	45% helix, 17% strand	Q2XVP4
D	Uncharacterized protein	protein	421	49% helix, 19% strand	F2Z5B2
E	Stathmin-4	protein	121	76% helix, 13% strand	P63043
F	Uncharacterized protein	protein	334	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
LXL · 1-ethyl-3-[2-methoxy-4-(5-methyl-4-{[(1S)-1-(pyridin-3-yl)butyl]amino}pyrimidin-2-yl)phenyl]urea · ligand · 2 copies · chains A, B, C, D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
CA · Calcium ion · metal · 2 copies · chains A, C
GOL · Glycerol · additive · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	779	0.85	0.88	103	GTP, MG, LXL
2	1139	0.85	0.86	116	GTP, MG, LXL
3	671	0.82	0.87	88	GDP, MG
4	166	0.79	0.95	37	empty
5	71	0.72	0.97	22	empty

Interfaces

9 interfaces between chains.

A–E · 1576 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1521 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1396 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 904 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 816 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5CA0 · Crystal structure of T2R-TTL-Lexibulin 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 Q2XVP4
Every structure of UniProt F2Z5B2
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 5CA0 · PDBe 5CA0 · UniProt Q2XVP4 · UniProt F2Z5B2 · UniProt P63043 · UniProt E1BQ43

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