MolNFT v1 · #103028 · protein
Crystal structure of the human filamin a ig-like domains 20-21 in complex with migfilin peptide
4P3W · Filamin-a: “Crystal structure of the human filamin a ig-like domains 20-21 in complex with migfilin peptide”. X-ray diffraction, 3 ligands (PR, NA, SO4), 15 pockets (best druggability 0.83). MolNFT v1 #103028 on GenesisL1: 3D…
- PDB
- 4P3W
- Type
- protein
- Length
- 1,090 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Filamin-a; Filamin-binding lim protein 1
- UniProt
- P21333, Q8WUP2
- Ligands
- PR, NA, SO4
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Filamin-a | protein | 172 | 5% helix, 50% strand | P21333 |
| B | Filamin-a | protein | 171 | 5% helix, 50% strand | P21333 |
| G, H, K | Filamin-binding lim protein 1 | protein | 15 | 0% helix, 60% strand | Q8WUP2 |
| E, C | Filamin-a | protein | 172 | 5% helix, 52% strand | P21333 |
| F | Filamin-a | protein | 157 | 4% helix, 53% strand | P21333 |
| L | Filamin-binding lim protein 1 | protein | 12 | 0% helix, 75% strand | Q8WUP2 |
| D | Filamin-a | protein | 162 | 4% helix, 51% strand | P21333 |
| J | Filamin-binding lim protein 1 | protein | 13 | 0% helix, 69% strand | Q8WUP2 |
| I | Filamin-binding lim protein 1 | protein | 14 | 0% helix, 64% strand | Q8WUP2 |
Ligands and binding sites
- PR · Praseodymium ion · metal · 4 copies · chains B, E, F, D, C
- NA · Sodium ion · metal · 2 copies · chains E, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.83 | 0.97 | 47 | empty |
| 2 | 206 | 0.82 | 0.96 | 46 | empty |
| 3 | 194 | 0.81 | 0.96 | 39 | empty |
| 4 | 1073 | 0.77 | 0.79 | 120 | empty |
| 5 | 439 | 0.66 | 0.78 | 67 | empty |
Interfaces
19 interfaces between chains.
- A–B · 1378 Ų buried · 17 hydrogen bonds · protein-protein
- D–C · 1360 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1274 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 910 Ų buried · 16 hydrogen bonds · protein-protein
- E–K · 900 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4P3W · Crystal structure of the human filamin A Ig-like domains 20-21 in complex with migfilin… · the same entry in another collection · chain I against I, 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 P21333
- Every structure of UniProt Q8WUP2
- Elsewhere: RCSB PDB 4P3W · PDBe 4P3W · UniProt P21333 · UniProt Q8WUP2
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