MolNFT v1 · #94710 · protein

Crystal structure of tubulin-RB3-ttl-zampanolide complex

4I4T · Tubulin alpha-1B chain: “Crystal structure of tubulin-RB3-ttl-zampanolide complex”. X-ray diffraction, 8 ligands (GTP, GDP, TYR), 20 pockets (best druggability 0.81). MolNFT v1 #94710 on GenesisL1: 3D structure, binding sites and…

PDB: 4I4T
Type: protein
Length: 2,218 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; Tubulin tyrosine ligase, ttl
UniProt: P81947, Q6B856, P63043, E1BQ43
Ligands: GTP, GDP, TYR, ZPN, ACP, MG, CA, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tubulin alpha-1B chain	protein	447	45% helix, 17% strand	P81947
B	Tubulin beta-2B chain	protein	420	49% helix, 20% strand	Q6B856
C	Tubulin alpha-1B chain	protein	440	46% helix, 17% strand	P81947
D	Tubulin beta-2B chain	protein	431	49% helix, 18% strand	Q6B856
E	Stathmin-4	protein	123	76% helix, 14% strand	P63043
F	Tubulin tyrosine ligase, ttl	protein	357	31% helix, 21% 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
TYR · Tyrosine · ligand · chains B, C
ZPN · (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide · ligand · chains D
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, F
CA · Calcium ion · metal · 4 copies · chains A, E, B, C
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 7 copies · chains A, B, E, F
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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	769	0.81	0.85	81	GTP, MG
2	626	0.80	0.86	86	GDP, MG
3	489	0.78	0.86	48	MG, ACP
4	1102	0.76	0.79	75	empty
5	406	0.76	0.86	56	GTP, MG

Interfaces

9 interfaces between chains.

A–E · 1604 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1452 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1436 Å² buried · 15 hydrogen bonds · protein-protein
A–F · 1409 Å² buried · 33 hydrogen bonds · protein-protein
B–C · 949 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4I4T · Crystal structure of tubulin-RB3-TTL-Zampanolide complex · the same entry in another collection · chain A against A, TM-score 1.00
Q6B856 · AlphaFold monomer V2.0 prediction for tubulin beta-2B chain (Q6B856) · a predicted model of the same protein · chain B against A, TM-score 0.99
P81947 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P81947) · 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 0.76

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 4I4T · PDBe 4I4T · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43

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