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Crystal structure of T2R-ttl-demecolcine complex

Analyse Crystal structure of T2R-ttl-demecolcine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XKE
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; Uncharacterized protein
UniProt: Q2XVP4, F2Z5B2, P63043, E1BQ43
Ligands: GTP, LON, GDP, MG, CA
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	437	43% helix, 19% strand	Q2XVP4
B	Tubulin beta chain	protein	428	48% helix, 19% strand	F2Z5B2
C	Tubulin alpha-1B chain	protein	440	45% helix, 16% strand	Q2XVP4
D	Tubulin beta chain	protein	421	48% 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 · 3 copies · chains A, B, C, D
LON · (7S)-1,2,3,10-tetramethoxy-7-(methylamino)-6,7-dihydro-5H-benzo[a]heptalen-9-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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	626	0.87	0.92	75	GTP, MG, LON
2	775	0.85	0.88	97	GTP, MG, LON
3	1171	0.83	0.84	119	GDP, MG
4	214	0.75	0.90	41	empty
5	890	0.72	0.77	63	empty

Interfaces

9 interfaces between chains.

A–E · 1651 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1492 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1411 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 953 Å² buried · 15 hydrogen bonds · protein-protein
A–F · 852 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5XKE · Crystal structure of T2R-TTL-Demecolcine 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 5XKE · PDBe 5XKE · UniProt Q2XVP4 · UniProt F2Z5B2 · UniProt P63043 · UniProt E1BQ43

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