MolNFT v1 · #133618 · protein
Tubulin-Z32400357-complex
5S5D · Tubulin alpha-1B chain: “Tubulin-Z32400357-complex”. X-ray diffraction, 6 ligands (GTP, GDP, NZJ), 20 pockets (best druggability 0.83). MolNFT v1 #133618 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5S5D
- Type
- protein
- Length
- 2,201 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, NZJ, ACP, MG, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 47% 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 | 423 | 48% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 48% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 431 | 49% helix, 18% strand | Q6B856 |
| E | Stathmin-4 | protein | 122 | 79% helix, 14% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 348 | 32% helix, 22% 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
- NZJ · 1-(3-methylbenzene-1-carbonyl)piperidine-4-carboxamide · ligand · 2 copies · chains B, C
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 5 copies · chains A, E, B, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.83 | 0.85 | 112 | GDP, MG, NZJ |
| 2 | 1000 | 0.83 | 0.84 | 114 | GTP, MG |
| 3 | 1022 | 0.80 | 0.81 | 107 | GTP, MG |
| 4 | 152 | 0.77 | 0.94 | 34 | empty |
| 5 | 80 | 0.71 | 0.96 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1593 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1424 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1361 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 939 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 816 Ų buried · 10 hydrogen bonds · protein-protein
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 5S5D · PDBe 5S5D · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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