Research workbench
Crystal structure of tubulin in complex with L-DM4-sme
Analyse Crystal structure of tubulin in complex with L-DM4-sme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E4Y
- Type
- protein
- Length
- 2,183 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, BKU, ACP, MG, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 45% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 430 | 47% helix, 18% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 439 | 45% helix, 18% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 423 | 48% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 77% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 331 | 34% helix, 22% 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
- BKU · (1S,2S,3S,5R,6S,16E,18E,20S,21R)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3, 5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl (2S)-2-{methyl[3-methyl-3-(methyldisulfanyl) butanoyl]amino}propanoate (non-preferred name) · ligand · chains D
- 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
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 | 969 | 0.82 | 0.83 | 109 | GTP, MG |
| 2 | 805 | 0.82 | 0.85 | 95 | GDP, MG |
| 3 | 201 | 0.81 | 0.95 | 43 | empty |
| 4 | 835 | 0.80 | 0.83 | 90 | GTP, MG |
| 5 | 88 | 0.73 | 0.96 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1591 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1477 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1447 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 925 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 811 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7E4Y · Crystal structure of tubulin in complex with L-DM4-SMe · 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 7E4Y · PDBe 7E4Y · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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