Research workbench

Tubulin-mmaf complex

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

PDB: 5J2U
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
UniProt: P81947, Q6B856, P63043
Ligands: GTP, GDP, 6DO, ACP, MG, CA
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	439	44% helix, 18% strand	P81947
B	Tubulin beta-2B chain	protein	428	47% helix, 18% strand	Q6B856
C	Tubulin alpha-1B chain	protein	440	48% helix, 17% strand	P81947
D	Tubulin beta-2B chain	protein	422	46% helix, 19% strand	Q6B856
E	Stathmin-4	protein	123	71% helix, 9% strand	P63043
F	Tubulin beta-2B chain	protein	344	31% helix, 22% strand	Q6B856

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
6DO · (2~{S})-2-[[(2~{R},3~{R})-3-methoxy-3-[(2~{S})-1-[(3~{R},4~{S},5~{S})-3-methoxy-5-methyl-4-[methyl-[(2~{S})-3-methyl-2-[[(2~{S})-3-methyl-2-(methylamino) butanoyl]amino]butanoyl]amino]heptanoyl]pyrrolidin-2-yl]-2-methyl-propanoyl]amino]-3-phenyl-propanoic acid · ligand · 2 copies · chains B, C, D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
CA · Calcium ion · metal · chains A

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	1157	0.82	0.83	115	GDP, MG, 6DO
2	1093	0.81	0.82	116	GTP, MG
3	1199	0.80	0.82	130	ACP
4	634	0.78	0.84	70	GTP, MG
5	209	0.77	0.92	34	empty

Interfaces

9 interfaces between chains.

A–E · 1590 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1411 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1389 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 974 Å² buried · 17 hydrogen bonds · protein-protein
A–F · 861 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5J2U · Tubulin-MMAF complex · the same entry in another collection · chain F against F, 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
Elsewhere: RCSB PDB 5J2U · PDBe 5J2U · UniProt P81947 · UniProt Q6B856 · UniProt P63043

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