Research workbench
Crystal structure of actin filament capping protein capz
Analyse Crystal structure of actin filament capping protein capz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IZN
- Type
- protein
- Length
- 1,088 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capz alpha-1 subunit; Capz beta-1 subunit
- UniProt
- P13127, P14315
- Ligands
- NO3
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capz alpha-1 subunit | protein | 275 | 38% helix, 30% strand | P13127 |
| B, D | Capz beta-1 subunit | protein | 270 | 42% helix, 32% strand | P14315 |
| C | Capz alpha-1 subunit | protein | 273 | 40% helix, 32% strand | P13127 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.74 | 0.78 | 108 | NO3 |
| 2 | 304 | 0.66 | 0.81 | 45 | NO3 |
| 3 | 291 | 0.65 | 0.81 | 40 | NO3 |
| 4 | 201 | 0.55 | 0.79 | 23 | empty |
| 5 | 235 | 0.54 | 0.77 | 29 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4017 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 3924 Ų buried · 60 hydrogen bonds · protein-protein
- B–D · 839 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 171 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1IZN · Crystal Structure of Actin Filament Capping Protein CapZ · the same entry in another collection · chain D against D, TM-score 1.00
- P13127 · AlphaFold monomer V2.0 prediction for F-actin-capping protein subunit alpha-1 (P13127) · a predicted model of the same protein · chain C against A, TM-score 0.92
- P14315 · AlphaFold monomer V2.0 prediction for F-actin-capping protein subunit beta isoforms 1 and… · a predicted model of the same protein · chain D against A, TM-score 0.91
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 P13127
- Every structure of UniProt P14315
- Elsewhere: RCSB PDB 1IZN · PDBe 1IZN · UniProt P13127 · UniProt P14315
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