Research workbench

Epd in complex with tubulin

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

PDB: 7DAD
Type: protein
Length: 2,209 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
UniProt: Q2XVP4, A0A287AGU7, P63042, E1BQ43
Ligands: GTP, GDP, EPD, ACP, MG, CA, CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	438	46% helix, 19% strand	Q2XVP4
B	Tubulin beta chain	protein	428	48% helix, 19% strand	A0A287AGU7
C	Tubulin alpha-1B chain	protein	440	47% helix, 18% strand	Q2XVP4
D	Tubulin beta chain	protein	431	48% helix, 18% strand	A0A287AGU7
E	Stathmin-4	protein	121	76% helix, 14% strand	P63042
F	Tubulin tyrosine ligase	protein	351	32% helix, 21% 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
EPD · Epothilone D · ligand · chains 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 · 4 copies · chains A, E, B, C
CL · Chloride ion · ion · chains A
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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1156	0.82	0.83	115	GDP, MG
2	769	0.82	0.85	94	empty
3	1069	0.79	0.81	115	GTP, MG
4	479	0.77	0.85	56	GTP, MG
5	936	0.73	0.77	71	empty

Interfaces

9 interfaces between chains.

A–E · 1645 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1451 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1369 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 880 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 823 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

7DAD · EPD in complex with tubulin · the same entry in another collection · chain C against C, TM-score 1.00
P63042 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63042) · a predicted model of the same protein · chain E against A, TM-score 0.75

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 P63042
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 7DAD · PDBe 7DAD · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63042 · UniProt E1BQ43

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