MolNFT v1 · #173156 · protein
Crystal structure of an anti-plasminogen activator inhibitor-1 (pai-1) scfv antibody fragment (scfv-33H1F7)
7AQL: “Crystal structure of an anti-plasminogen activator inhibitor-1 (pai-1) scfv antibody fragment (scfv-33H1F7)”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.72). MolNFT v1 #173156 on GenesisL1: 3D structure…
- PDB
- 7AQL
- Type
- protein
- Length
- 904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv-33H1F7
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Scfv-33H1F7 | protein | 225 | 5% helix, 52% strand | — |
| A, C | Scfv-33H1F7 | protein | 226 | 5% helix, 52% strand | — |
| D | Scfv-33H1F7 | protein | 227 | 5% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.72 | 0.81 | 55 | empty |
| 2 | 190 | 0.55 | 0.80 | 30 | empty |
| 3 | 169 | 0.50 | 0.78 | 36 | empty |
| 4 | 122 | 0.43 | 0.77 | 25 | empty |
| 5 | 127 | 0.42 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 800 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 484 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 340 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7AQL · Crystal Structure of an Anti-Plasminogen Activator Inhibitor-1 (PAI-1) scFv antibody… · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 7AQL · PDBe 7AQL
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