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Complex of novel maytansinoid M24 bound to T2R-ttl (two tubulin ALPHA/BETA heterodimers, RB3 stathmin-like domain, and tubulin tyrosine ligase)

Analyse Complex of novel maytansinoid M24 bound to T2R-ttl (two tubulin ALPHA/BETA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7L05
Type: protein
Length: 2,183 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, P02554, P63043, E1BQ43
Ligands: GTP, GDP, XQ4, ACP, MG, CA, CL
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	439	46% helix, 18% strand	Q2XVP4
B	Tubulin beta chain	protein	421	49% helix, 19% strand	P02554
C	Tubulin alpha-1B chain	protein	440	46% helix, 16% strand	Q2XVP4
D	Tubulin beta chain	protein	420	49% helix, 19% strand	P02554
E	Stathmin-4	protein	121	76% helix, 14% strand	P63043
F	Tubulin tyrosine ligase	protein	342	32% helix, 22% 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
XQ4 · (1S,2R,3S,5S,6S,16E,18E,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3, 5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl (2S)-2-{methyl[3-(methylamino)propanoyl]amino}propanoate (non-preferred name) · 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
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, E
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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	927	0.84	0.86	122	GDP, MG
2	918	0.82	0.84	101	GTP, MG
3	205	0.80	0.94	45	empty
4	529	0.78	0.86	61	GTP, MG
5	804	0.74	0.79	77	empty

Interfaces

9 interfaces between chains.

A–E · 1665 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1471 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1436 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 903 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 850 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7L05 · Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers… · 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 Q2XVP4
Every structure of UniProt P02554
Every structure of UniProt P63043
Every structure of UniProt E1BQ43
Elsewhere: RCSB PDB 7L05 · PDBe 7L05 · UniProt Q2XVP4 · UniProt P02554 · UniProt P63043 · UniProt E1BQ43

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