MolNFT v1 · #99173 · protein
Crystal structure of PFSUB1-prodomain-NIMP.M7 Fab complex
4LVN · Subtilisin-like serine protease: “Crystal structure of PFSUB1-prodomain-NIMP.M7 Fab complex”. X-ray diffraction, 2 ligands (CA, NI), 6 pockets (best druggability 0.64). MolNFT v1 #99173 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4LVN
- Type
- protein
- Length
- 840 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, NI
- Pockets
- 6 · best druggability 0.64
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 | 207 | 5% helix, 51% strand | — |
| C | NIMP.M7 Fab heavy chain | protein | 216 | 4% helix, 52% strand | — |
| P | Subtilisin-like serine protease (EC 3.4.21.61) | protein | 81 | 38% helix, 32% strand | Q868D6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.64 | 0.78 | 52 | empty |
| 2 | 266 | 0.51 | 0.75 | 45 | empty |
| 3 | 65 | 0.41 | 0.81 | 17 | empty |
| 4 | 71 | 0.34 | 0.76 | 18 | empty |
| 5 | 64 | 0.29 | 0.74 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1716 Ų buried · 16 hydrogen bonds · protein-protein
- A–P · 1193 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 531 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 4LVN · Crystal structure of PfSUB1-prodomain-NIMP.M7 Fab complex · 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 4LVN · PDBe 4LVN · UniProt Q868D6
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