Research workbench
Antibody 2F2 in complex with P. vivax csp peptide gdraagqpagdraagqpa
Analyse Antibody 2F2 in complex with P. vivax csp peptide gdraagqpagdraagqpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RLW
- Type
- protein
- Length
- 901 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PVCSPVK210 peptide from circumsporozoite protein; 2F2 Fab light chain; 2F2 Fab heavy chain
- UniProt
- P08677
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | PVCSPVK210 peptide from circumsporozoite protein | protein | 12 | 0% helix, 0% strand | P08677 |
| B | 2F2 Fab light chain | protein | 219 | 6% helix, 52% strand | — |
| A | 2F2 Fab heavy chain | protein | 222 | 10% helix, 52% strand | — |
| D | 2F2 Fab light chain | protein | 218 | 6% helix, 52% strand | — |
| C | 2F2 Fab heavy chain | protein | 220 | 10% helix, 54% strand | — |
| R | PVCSPVK210 peptide from circumsporozoite protein | protein | 10 | 30% helix, 0% strand | P08677 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.61 | 0.74 | 65 | empty |
| 2 | 506 | 0.61 | 0.75 | 59 | empty |
| 3 | 50 | 0.53 | 0.89 | 20 | empty |
| 4 | 191 | 0.47 | 0.74 | 24 | empty |
| 5 | 112 | 0.46 | 0.79 | 22 | empty |
Interfaces
11 interfaces between chains.
- B–A · 2258 Ų buried · 19 hydrogen bonds · protein-protein
- D–C · 2162 Ų buried · 19 hydrogen bonds · protein-protein
- P–A · 524 Ų buried · 6 hydrogen bonds · protein-protein
- C–R · 502 Ų buried · 5 hydrogen bonds · protein-protein
- D–R · 340 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 7RLW · Antibody 2F2 in complex with P. vivax CSP peptide GDRAAGQPAGDRAAGQPA · the same entry in another collection · chain R against R, TM-score 1.00
- P08677 · AlphaFold monomer V2.0 prediction for circumsporozoite protein (P08677) · a predicted model of the same protein · chain R against A, TM-score 0.33
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 P08677
- Elsewhere: RCSB PDB 7RLW · PDBe 7RLW · UniProt P08677
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