MolNFT v1 · #139516 · protein

Crystal structure of T2R-ttl-PO5 complex

5XI5 · Tubulin alpha chain: “Crystal structure of T2R-ttl-PO5 complex”. X-ray diffraction, 6 ligands (GTP, PN6, GDP), 20 pockets (best druggability 0.86). MolNFT v1 #139516 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XI5
Type: protein
Length: 2,151 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: A0A0R4I993, A0A0R4I995, P63043, E1BQ43
Ligands: GTP, PN6, GDP, ACP, 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 chain	protein	437	45% helix, 19% strand	A0A0R4I993
B	Tubulin beta chain	protein	424	49% helix, 20% strand	A0A0R4I995
C	Tubulin alpha chain	protein	440	45% helix, 17% strand	A0A0R4I993
D	Tubulin beta chain	protein	421	48% helix, 19% strand	A0A0R4I995
E	Stathmin-4	protein	120	77% helix, 14% strand	P63043
F	Tubulin tyrosine ligase	protein	309	28% helix, 25% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
PN6 · (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione · ligand · 2 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · chains B
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 3 copies · chains A, B, C
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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	771	0.86	0.90	92	GTP, MG, PN6
2	882	0.84	0.86	104	GTP, MG, PN6
3	947	0.83	0.85	114	GDP, MG
4	149	0.78	0.96	32	empty
5	855	0.72	0.77	67	empty

Interfaces

9 interfaces between chains.

A–E · 1596 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1551 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1474 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 920 Å² buried · 12 hydrogen bonds · protein-protein
C–E · 868 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5XI5 · Crystal structure of T2R-TTL-PO5 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 A0A0R4I993
Every structure of UniProt A0A0R4I995
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 5XI5 · PDBe 5XI5 · UniProt A0A0R4I993 · UniProt A0A0R4I995 · UniProt P63043 · UniProt E1BQ43

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