MolNFT v1 · #177019 · protein
Crystal structure of tubulin in complex with maytansinol
7E4Z · Tubulin alpha-1B chain: “Crystal structure of tubulin in complex with maytansinol”. X-ray diffraction, 7 ligands (GTP, GDP, BKL), 20 pockets (best druggability 0.82). MolNFT v1 #177019 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7E4Z
- 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-2B chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, BKL, ACP, MG, CA, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tubulin alpha-1B chain | protein | 440 | 45% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 425 | 48% helix, 19% strand | Q6B856 |
| D | Tubulin beta-2B chain | protein | 421 | 49% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 76% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 348 | 31% helix, 23% 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
- BKL · (1R,2S,3S,5S,6S,16E,18E,20R,21S)-11-chloro-6,21-dihydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3, 5~]hexacosa-10(26),11,13,16,18-pentaene-8,23-dione · ligand · chains D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, E
- CL · Chloride ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, E
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.82 | 0.86 | 89 | GDP, MG |
| 2 | 1062 | 0.81 | 0.82 | 118 | GTP, MG |
| 3 | 229 | 0.81 | 0.94 | 42 | empty |
| 4 | 954 | 0.80 | 0.82 | 97 | GTP, MG |
| 5 | 1154 | 0.75 | 0.78 | 88 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1614 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1406 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1395 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 876 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 869 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7E4Z · Crystal structure of tubulin in complex with Maytansinol · 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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 7E4Z · PDBe 7E4Z · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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