MolNFT v1 · #133803 · protein
Tubulin-maytansinoid-3-complex
5SB8 · Tubulin alpha-1B chain: “Tubulin-maytansinoid-3-complex”. X-ray diffraction, 6 ligands (GTP, GDP, 5IS), 20 pockets (best druggability 0.84). MolNFT v1 #133803 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5SB8
- Type
- protein
- Length
- 2,189 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, 5IS, ACP, MG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 438 | 45% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 422 | 48% helix, 19% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 427 | 49% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 77% helix, 14% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 339 | 33% helix, 24% 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
- 5IS · (1S,2R,3S,5S,6S,16E,18E,20R)-11-chloro-6-hydroxy-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),11,13,16,18,21-hexaene-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, F
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
- IMD · Imidazole · additive · chains 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.84 | 0.86 | 122 | GDP, MG |
| 2 | 1028 | 0.80 | 0.82 | 108 | GTP, MG |
| 3 | 183 | 0.77 | 0.93 | 33 | empty |
| 4 | 439 | 0.75 | 0.85 | 56 | GTP, MG |
| 5 | 1076 | 0.75 | 0.78 | 92 | MG |
Interfaces
9 interfaces between chains.
- A–E · 1599 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1421 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1308 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 909 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 819 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5SB8 · Tubulin-maytansinoid-3-complex · 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 5SB8 · PDBe 5SB8 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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