MolNFT v1 · #179905 · protein
Plasmodium falciparum protein PF12P bound to nanobody B9
7KJH: “Plasmodium falciparum protein PF12P bound to nanobody B9”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.74). MolNFT v1 #179905 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KJH
- Type
- protein
- Length
- 767 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody B9; Surface protein P12P
- UniProt
- C6KSX1
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody B9 | protein | 120 | 3% helix, 53% strand | — |
| C | Surface protein P12P | protein | 261 | 7% helix, 49% strand | C6KSX1 |
| D | Surface protein P12P | protein | 260 | 7% helix, 48% strand | C6KSX1 |
| B | Nanobody B9 | protein | 126 | 2% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, D
- FLC · Citrate anion · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.74 | 0.82 | 58 | FLC |
| 2 | 157 | 0.52 | 0.79 | 38 | empty |
| 3 | 77 | 0.50 | 0.84 | 17 | empty |
| 4 | 63 | 0.46 | 0.83 | 17 | empty |
| 5 | 165 | 0.46 | 0.76 | 30 | empty |
Interfaces
4 interfaces between chains.
- D–B · 1024 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 984 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 196 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 C6KSX1
- Elsewhere: RCSB PDB 7KJH · PDBe 7KJH · UniProt C6KSX1
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