Research workbench
Complex of Fab 2/6.14 with domain 3 of P. berghei HAP2
Analyse Complex of Fab 2/6.14 with domain 3 of P. berghei HAP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LR3
- Type
- protein
- Length
- 1,032 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D3_2/6.14 Fab light chain; D3_2/6.14 Fab heavy chain; Hapless 2
- UniProt
- Q4YCF6
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | D3_2/6.14 Fab light chain | protein | 210 | 7% helix, 50% strand | — |
| H | D3_2/6.14 Fab heavy chain | protein | 209 | 4% helix, 54% strand | — |
| D | Hapless 2 | protein | 110 | 0% helix, 54% strand | Q4YCF6 |
| C | Hapless 2 | protein | 80 | 0% helix, 56% strand | Q4YCF6 |
| A | D3_2/6.14 Fab heavy chain | protein | 214 | 6% helix, 52% strand | — |
| B | D3_2/6.14 Fab light chain | protein | 209 | 7% helix, 52% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.76 | 0.80 | 91 | empty |
| 2 | 849 | 0.74 | 0.78 | 74 | empty |
| 3 | 422 | 0.69 | 0.81 | 43 | empty |
| 4 | 749 | 0.67 | 0.75 | 69 | empty |
| 5 | 568 | 0.61 | 0.74 | 59 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1793 Ų buried · 12 hydrogen bonds · protein-protein
- L–H · 1789 Ų buried · 14 hydrogen bonds · protein-protein
- H–D · 639 Ų buried · 10 hydrogen bonds · protein-protein
- C–A · 635 Ų buried · 11 hydrogen bonds · protein-protein
- H–A · 453 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 modified (disulfide, oxidation).
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 Q4YCF6
- Elsewhere: RCSB PDB 7LR3 · PDBe 7LR3 · UniProt Q4YCF6
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