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Structure of tubulin tyrosine ligase in complex with TB116

Analyse Structure of tubulin tyrosine ligase in complex with TB116 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Y4N
Type: protein
Length: 2,207 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, O9B, O9K, O9N, VAL, P6S, ACP, MG, CA
Pockets: 20 · best druggability 0.82

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	45% helix, 18% strand	Q2XVP4
B	Tubulin beta chain	protein	431	49% helix, 19% strand	P02554
C	Tubulin alpha-1B chain	protein	440	47% helix, 17% strand	Q2XVP4
D	Tubulin beta chain	protein	428	49% helix, 19% strand	P02554
E	Stathmin-4	protein	123	77% helix, 13% strand	P63043
F	Tubulin-tyrosine ligase	protein	346	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
O9B · (2~{R})-1-methylpiperidine-2-carboxylic acid · ligand · chains B, C
O9K · [(1~{R},3~{R})-1-(4-methanoyl-1,3-thiazol-2-yl)-4-methyl-3-(methylamino)pentyl] ethanoate · ligand · chains B, C
O9N · methyl (2~{S},4~{S})-2,4-bis(azanyl)-5-phenyl-pentanoate · ligand · chains B
VAL · Valine · ligand · chains B, C
P6S · benzyl hydrogen carbonate · ligand · chains B, C
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 2 copies · chains A, C
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
PGE · Triethylene glycol · additive · chains C
PEG · Di(hydroxyethyl)ether · additive · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	870	0.82	0.85	103	GTP, MG
2	1019	0.82	0.83	93	GDP, MG, O9B, O9K, VAL
3	1050	0.81	0.82	117	GTP, MG
4	168	0.79	0.95	29	empty
5	1177	0.75	0.78	82	empty

Interfaces

9 interfaces between chains.

A–E · 1606 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1457 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1430 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 899 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 857 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6Y4N · Structure of Tubulin Tyrosine Ligase in Complex with Tb116 · the same entry in another collection · chain F against F, TM-score 1.00
P02554 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02554) · a predicted model of the same protein · chain D against A, TM-score 0.98
Q2XVP4 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (Q2XVP4) · a predicted model of the same protein · chain C against A, TM-score 0.96
P63043 · AlphaFold monomer V2.0 prediction for stathmin-4 (P63043) · a predicted model of the same protein · chain E against A, TM-score 0.77

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 6Y4N · PDBe 6Y4N · UniProt Q2XVP4 · UniProt P02554 · UniProt P63043 · UniProt E1BQ43

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