MolNFT v1 · #139593 · protein

Crystal structure of T2R-ttl-CH1 complex

5XKG · Tubulin alpha-1B chain: “Crystal structure of T2R-ttl-CH1 complex”. X-ray diffraction, 5 ligands (GTP, 890, GDP), 20 pockets (best druggability 0.86). MolNFT v1 #139593 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XKG
Type: protein
Length: 2,181 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, P63043, E1BQ43
Ligands: GTP, 890, GDP, MG, CA
Pockets: 20 · best druggability 0.86

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	45% helix, 18% strand	Q2XVP4
B	Tubulin beta chain	protein	428	48% helix, 18% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	46% helix, 17% strand	Q2XVP4
D	Tubulin beta chain	protein	421	49% helix, 19% strand	A0A287AGU7
E	Stathmin-4	protein	121	76% helix, 14% strand	P63043
F	Tubulin tyrosine ligase	protein	334	30% helix, 22% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, C, D
890 · 4-[(3-azanyl-4-methoxy-phenyl)-methyl-amino]chromen-2-one · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · chains B
MG · Magnesium ion · metal · 4 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	1057	0.86	0.87	118	GTP, MG, 890
2	1090	0.83	0.84	121	GTP, MG, 890
3	857	0.83	0.85	103	GDP, MG
4	159	0.78	0.94	36	empty
5	825	0.72	0.77	64	empty

Interfaces

9 interfaces between chains.

A–E · 1617 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1492 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1399 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 895 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 832 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5XKG · Crystal structure of T2R-TTL-CH1 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 A0A287AGU7
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 5XKG · PDBe 5XKG · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43

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