Research workbench

Tubulin-Z106307058-complex

Analyse Tubulin-Z106307058-complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5S55
Type: protein
Length: 2,201 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, WZP, ACP, MG, CA
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	438	47% helix, 18% strand	P81947
B	Tubulin beta-2B chain	protein	425	50% helix, 19% strand	Q6B856
C	Tubulin alpha-1B chain	protein	440	46% helix, 17% strand	P81947
D	Tubulin beta-2B chain	protein	426	49% helix, 19% strand	Q6B856
E	Stathmin-4	protein	123	78% helix, 14% 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
WZP · 2-methyl-1-[4-(propan-2-yl)piperazin-1-yl]propan-1-one · ligand · 2 copies · chains A, B, C, D, E
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 4 copies · chains A, E, B, C

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	905	0.84	0.86	117	GDP, MG
2	933	0.82	0.84	108	GTP, MG
3	834	0.79	0.82	94	GTP, MG
4	161	0.78	0.94	33	empty
5	1076	0.74	0.77	82	MG

Interfaces

9 interfaces between chains.

A–E · 1624 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1455 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1427 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 927 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 824 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5S55 · Tubulin-Z106307058-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 P81947
Every structure of UniProt Q6B856
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 5S55 · PDBe 5S55 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43

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