MolNFT v1 · #181677 · protein

18-mer hela-tubulin rings in complex with cryptophycin 1

7M20 · Tubulin beta-3 chain: “18-mer hela-tubulin rings in complex with cryptophycin 1”. Electron microscopy, 3 ligands (GDP, YNP, GTP), 20 pockets (best druggability 0.84). MolNFT v1 #181677 on GenesisL1: 3D structure, binding sites and…

PDB: 7M20
Type: protein
Length: 7,785 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tubulin beta-3 chain; Tubulin alpha-1B chain
UniProt: Q13509, P68363
Ligands: GDP, YNP, GTP
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 2 distinct chains · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D, F, H, J, L, N, P, R	Tubulin beta-3 chain	protein	429	43% helix, 16% strand	Q13509
A, C, E, G, I, K, M, O, Q	Tubulin alpha-1B chain	protein	436	41% helix, 10% strand	P68363

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 9 copies · chains B, D, F, H, J, L, N, P, R
YNP · Cryptophycin 1 · ligand · 9 copies · chains B, A, D, C, F, E, H, G, J, I, L, K, N, M, P, O, R, Q
GTP · Guanosine-5'-triphosphate · ligand · 9 copies · chains A, C, E, G, I, K, M, O, Q

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1012	0.84	0.85	92	GTP
2	1137	0.82	0.83	100	GTP
3	1098	0.82	0.83	93	GTP
4	1096	0.82	0.83	97	GTP
5	1190	0.81	0.83	105	GTP

Interfaces

18 interfaces between chains.

N–O · 901 Å² buried · 1 hydrogen bond · protein-protein
D–E · 898 Å² buried · 1 hydrogen bond · protein-protein
B–C · 897 Å² buried · 1 hydrogen bond · protein-protein
F–G · 897 Å² buried · 1 hydrogen bond · protein-protein
H–I · 897 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7M20 · 18-mer HeLa-tubulin rings in complex with Cryptophycin 1 · the same entry in another collection · chain Q against Q, 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 Q13509
Every structure of UniProt P68363
Elsewhere: RCSB PDB 7M20 · PDBe 7M20 · UniProt Q13509 · UniProt P68363

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