MolNFT v1 · #148913 · protein

Tubulin-TUB015 complex

6FKL · Tubulin alpha-1B chain: “Tubulin-TUB015 complex”. X-ray diffraction, 6 ligands (GTP, GDP, DLK), 20 pockets (best druggability 0.85). MolNFT v1 #148913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6FKL
Type: protein
Length: 2,196 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: P81947, Q6B856, P63043, E1BQ43
Ligands: GTP, GDP, DLK, 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	439	47% helix, 18% strand	P81947
B	Tubulin beta-2B chain	protein	425	48% helix, 20% strand	Q6B856
C	Tubulin alpha-1B chain	protein	439	47% helix, 17% strand	P81947
D	Tubulin beta-2B chain	protein	422	50% helix, 19% strand	Q6B856
E	Stathmin-4	protein	122	77% helix, 13% strand	P63043
F	Tubulin tyrosine ligase	protein	349	32% 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
DLK · 2-{1-[(2-Methoxyphenyl)amino]ethylidene}-5-phenyl-1,3-cyclohexanedione · ligand · 2 copies · chains A, B, C, D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 5 copies · chains A, E, B, C
GOL · Glycerol · additive · 2 copies · chains A, B
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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	981	0.85	0.86	118	GTP, MG, DLK
2	1185	0.82	0.83	128	GDP, MG, GOL
3	990	0.82	0.83	99	MG, ACP
4	1070	0.82	0.83	126	GTP, MG, DLK
5	211	0.81	0.95	45	empty

Interfaces

9 interfaces between chains.

A–E · 1586 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1479 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1477 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 921 Å² buried · 17 hydrogen bonds · protein-protein
A–F · 837 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6FKL · Tubulin-TUB015 complex · the same entry in another collection · chain D against D, 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 P81947
Every structure of UniProt Q6B856
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 6FKL · PDBe 6FKL · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43

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