Research workbench
Matcap bound to a human 14 protofilament microtubule
Analyse Matcap bound to a human 14 protofilament microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Z6S
- Type
- protein
- Length
- 2,392 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-3 chain; Uncharacterized protein KIAA0895-like
- UniProt
- P68363, Q13509, Q68EN5
- Ligands
- GTP, GDP, MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | Tubulin alpha-1B chain | protein | 435 | 44% helix, 14% strand | P68363 |
| B, H | Tubulin beta-3 chain | protein | 429 | 48% helix, 17% strand | Q13509 |
| C, E | Uncharacterized protein KIAA0895-like | protein | 332 | 55% helix, 7% strand | Q68EN5 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, H, B, K
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B, H
- MG · Magnesium ion · metal · 2 copies · chains A, K
- ZN · Zinc ion · metal · 2 copies · chains C, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.84 | 0.94 | 50 | GDP |
| 2 | 259 | 0.82 | 0.94 | 44 | GTP, MG |
| 3 | 246 | 0.82 | 0.95 | 42 | GTP, MG |
| 4 | 890 | 0.78 | 0.81 | 86 | ZN |
| 5 | 796 | 0.77 | 0.81 | 74 | ZN |
Interfaces
6 interfaces between chains.
- A–H · 2033 Ų buried · 19 hydrogen bonds · protein-protein
- B–K · 2024 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1860 Ų buried · 18 hydrogen bonds · protein-protein
- K–C · 771 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 697 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7Z6S · MATCAP bound to a human 14 protofilament microtubule · the same entry in another collection · chain E against E, TM-score 1.00
- P68363 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P68363) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q68EN5 · AlphaFold monomer V2.0 prediction for uncharacterized protein KIAA0895-like (Q68EN5) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q13509 · AlphaFold monomer V2.0 prediction for tubulin beta-3 chain (Q13509) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P68363
- Every structure of UniProt Q13509
- Every structure of UniProt Q68EN5
- Elsewhere: RCSB PDB 7Z6S · PDBe 7Z6S · UniProt P68363 · UniProt Q13509 · UniProt Q68EN5
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