MolNFT v1 · #99174 · protein
Crystal structure of PFSUB1-prodomain-NIMP.M7 Fab complex with added CACL2
4LVO · Subtilisin-like serine protease: “Crystal structure of PFSUB1-prodomain-NIMP.M7 Fab complex with added CACL2”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.66). MolNFT v1 #99174 on GenesisL1: 3D structure…
- PDB
- 4LVO
- Type
- protein
- Length
- 841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilisin-like serine protease; NIMP.M7 Fab light chain; NIMP.M7 Fab heavy chain
- EC
- 3.4.21.61
- UniProt
- Q868D6
- Ligands
- CA
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Subtilisin-like serine protease (EC 3.4.21.61) | protein | 336 | 32% helix, 22% strand | Q868D6 |
| B | NIMP.M7 Fab light chain | protein | 212 | 5% helix, 52% strand | — |
| C | NIMP.M7 Fab heavy chain | protein | 214 | 6% helix, 52% strand | — |
| P | Subtilisin-like serine protease (EC 3.4.21.61) | protein | 79 | 37% helix, 33% strand | Q868D6 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.66 | 0.78 | 57 | empty |
| 2 | 121 | 0.42 | 0.76 | 24 | empty |
| 3 | 50 | 0.41 | 0.83 | 14 | empty |
| 4 | 142 | 0.40 | 0.74 | 23 | empty |
| 5 | 58 | 0.32 | 0.76 | 13 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1773 Ų buried · 15 hydrogen bonds · protein-protein
- A–P · 1204 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 329 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4LVO · Crystal structure of PfSUB1-prodomain-NIMP.M7 Fab complex with added CaCl2 · the same entry in another collection · chain A against A, 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 Q868D6
- Elsewhere: RCSB PDB 4LVO · PDBe 4LVO · UniProt Q868D6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.