Research workbench

Tubulin-RB3_SLD-ttl in complex with heterocyclic pyrimidine compound 4A

Analyse Tubulin-RB3_SLD-ttl in complex with heterocyclic pyrimidine compound 4A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BR1
Type: protein
Length: 2,178 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, Q9H169, E1BQ43
Ligands: GTP, GDP, E3Y, ACP, MG, CA
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	437	46% helix, 18% strand	Q2XVP4
B	Tubulin beta-2B chain	protein	427	48% helix, 20% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	47% helix, 17% strand	Q2XVP4
D	Tubulin beta-2B chain	protein	421	49% helix, 19% strand	A0A287AGU7
E	Stathmin-4	protein	121	76% helix, 13% strand	Q9H169
F	Tubulin tyrosine ligase	protein	332	31% helix, 23% 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
E3Y · 2-chloro-4-(6-methoxy-3,4-dihydroquinolin-1(2H)-yl) pyrido[2,3-d]pyrimidine · ligand · 2 copies · chains A, B, C, D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 4 copies · chains A, B, C, F
CA · Calcium ion · metal · 2 copies · chains A, 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	334	0.85	0.95	60	GTP, MG, E3Y
2	851	0.85	0.88	116	GTP, MG, E3Y
3	582	0.80	0.86	77	GDP, MG
4	151	0.76	0.94	32	empty
5	330	0.73	0.85	48	empty

Interfaces

9 interfaces between chains.

A–E · 1628 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1492 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1397 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 883 Å² buried · 15 hydrogen bonds · protein-protein
C–E · 796 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6BR1 · Tubulin-RB3_SLD-TTL in complex with heterocyclic pyrimidine compound 4a · the same entry in another collection · chain C against C, TM-score 1.00
Q9H169 · AlphaFold monomer V2.0 prediction for stathmin-4 (Q9H169) · 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 Q9H169
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 6BR1 · PDBe 6BR1 · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt Q9H169 · UniProt E1BQ43

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