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Crystal structure of tubulin in complex with Maytansinol

Analyse Crystal structure of tubulin in complex with Maytansinol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E4Z
Type: protein
Length: 2,197 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.69
Source: Bos taurus; Gallus gallus; Rattus norvegicus
Molecule: Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: P81947, Q6B856, P63043, E1BQ43
Ligands: GTP, GDP, BKL, ACP, MG, CA, CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · resolution 2.69 · 5 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Tubulin alpha-1B chain	protein	440	45% helix, 18% strand	P81947
B	Tubulin beta-2B chain	protein	425	48% helix, 19% strand	Q6B856
D	Tubulin beta-2B chain	protein	421	49% helix, 19% strand	Q6B856
E	Stathmin-4	protein	123	76% helix, 13% strand	P63043
F	Tubulin tyrosine ligase	protein	348	31% helix, 23% strand	E1BQ43

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
GDP · Guanosine-5'-diphosphate · ligand · chains B
BKL · (1R,2S,3S,5S,6S,16E,18E,20R,21S)-11-chloro-6,21-dihydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3, 5~]hexacosa-10(26),11,13,16,18-pentaene-8,23-dione · ligand · chains D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, E
CL · Chloride ion · ion · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, E

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	679	0.82	0.86	89	GDP, MG
2	1062	0.81	0.82	118	GTP, MG
3	229	0.81	0.94	42	empty
4	954	0.80	0.82	97	GTP, MG
5	1154	0.75	0.78	88	empty

Interfaces

9 interfaces between chains.

A–E · 1614 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1406 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1395 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 876 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 869 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7E4Z · Crystal structure of tubulin in complex with maytansinol · the same entry in another collection · chain C against C, TM-score 1.00
P81947 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P81947) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 7E4Z · PDBe 7E4Z · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43

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