Research workbench
Human metavinculin mvt Q971R, R975D, T978R mutant (residues 959-1134) in complex with PIP2
Analyse Human metavinculin mvt Q971R, R975D, T978R mutant (residues 959-1134) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L0G
- Type
- protein
- Length
- 685 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin
- UniProt
- P18206
- Ligands
- PIO
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 172 | 73% helix, 2% strand | P18206 |
| B | Vinculin | protein | 172 | 74% helix, 2% strand | P18206 |
| C | Vinculin | protein | 171 | 76% helix, 2% strand | P18206 |
| D | Vinculin | protein | 170 | 75% helix, 2% strand | P18206 |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.77 | 0.82 | 73 | empty |
| 2 | 162 | 0.60 | 0.83 | 27 | empty |
| 3 | 112 | 0.47 | 0.79 | 19 | empty |
| 4 | 54 | 0.31 | 0.76 | 12 | empty |
| 5 | 65 | 0.28 | 0.73 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–C · 653 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 377 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 341 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 142 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5L0G · Human metavinculin MVt Q971R, R975D, T978R mutant (residues 959-1134) in complex with PIP2 · the same entry in another collection · chain D against D, TM-score 1.00
- P18206 · AlphaFold monomer V2.0 prediction for vinculin (P18206) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P18206
- Elsewhere: RCSB PDB 5L0G · PDBe 5L0G · UniProt P18206
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