MolNFT v1 · #177010 · protein
Crystal structure of tubulin in complex with L-DM1-sme
7E4Q · Tubulin alpha-1B chain: “Crystal structure of tubulin in complex with L-DM1-sme”. X-ray diffraction, 6 ligands (GTP, GDP, BKX), 20 pockets (best druggability 0.82). MolNFT v1 #177010 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7E4Q
- Type
- protein
- Length
- 2,184 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, BKX, 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 | 437 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 430 | 47% helix, 18% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 424 | 48% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 77% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 330 | 34% 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
- BKX · (1S,2R,3R,5R,6R,16E,18E,20R,21S)-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-(methyldisulfanyl)propanoyl]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 | 782 | 0.82 | 0.85 | 92 | GTP, MG |
| 2 | 1008 | 0.80 | 0.82 | 104 | GDP, MG |
| 3 | 1032 | 0.80 | 0.81 | 110 | GTP, MG |
| 4 | 218 | 0.77 | 0.92 | 43 | empty |
| 5 | 856 | 0.72 | 0.77 | 64 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1591 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1469 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1422 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 926 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 815 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7E4Q · Crystal structure of tubulin in complex with L-DM1-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 7E4Q · PDBe 7E4Q · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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