MolNFT v1 · #112319 · protein

Crystal structure of tubulin-stathmin-ttl-mmae complex

4ZHQ · Tubulin alpha-1B chain: “Crystal structure of tubulin-stathmin-ttl-mmae complex”. X-ray diffraction, 6 ligands (GTP, GDP, 4Q5), 20 pockets (best druggability 0.82). MolNFT v1 #112319 on GenesisL1: 3D structure, binding sites and…

PDB: 4ZHQ
Type: protein
Length: 2,197 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, 4Q5, ACP, MG, CA
Pockets: 20 · best druggability 0.82

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	439	46% helix, 18% strand	Q2XVP4
B	Tubulin beta chain	protein	427	48% helix, 18% strand	P02554
C	Tubulin alpha-1B chain	protein	440	47% helix, 16% strand	Q2XVP4
D	Tubulin beta chain	protein	422	49% helix, 19% strand	P02554
E	Stathmin-4	protein	123	76% helix, 13% strand	P63043
F	Tubulin-tyrosine ligase	protein	346	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
4Q5 · N-methyl-L-valyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide · ligand · chains B, C
ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 3 copies · chains A, B, C
GOL · Glycerol · additive · 8 copies · chains A, E, B, C
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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1126	0.82	0.83	117	GDP, MG, 4Q5, GOL
2	890	0.81	0.84	100	GTP, MG, GOL
3	1080	0.81	0.82	117	GTP, MG, GOL
4	162	0.78	0.95	33	empty
5	1146	0.75	0.78	77	empty

Interfaces

9 interfaces between chains.

A–E · 1638 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1428 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1376 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 982 Å² buried · 18 hydrogen bonds · protein-protein
A–F · 823 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4ZHQ · Crystal structure of Tubulin-Stathmin-TTL-MMAE Complex · 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 4ZHQ · PDBe 4ZHQ · UniProt Q2XVP4 · UniProt P02554 · UniProt P63043 · UniProt E1BQ43

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