Research workbench
Antibody 2F2 in complex with P. vivax csp peptide gdraagqpagngaggqaa
Analyse Antibody 2F2 in complex with P. vivax csp peptide gdraagqpagngaggqaa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RLZ
- Type
- protein
- Length
- 897 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide from circumsporozoite protein variant VK210; 2F2 Fab light chain; 2F2 Fab heavy…
- UniProt
- P08677
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, R | Peptide from circumsporozoite protein variant VK210 | protein | 10 | 30% helix, 0% strand | P08677 |
| B, C | 2F2 Fab light chain | protein | 218 | 6% helix, 52% strand | — |
| A | 2F2 Fab heavy chain | protein | 221 | 10% helix, 55% strand | — |
| D | 2F2 Fab heavy chain | protein | 220 | 10% helix, 54% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.63 | 0.74 | 69 | empty |
| 2 | 371 | 0.54 | 0.74 | 50 | empty |
| 3 | 72 | 0.49 | 0.84 | 22 | empty |
| 4 | 144 | 0.43 | 0.75 | 22 | empty |
| 5 | 95 | 0.36 | 0.75 | 18 | empty |
Interfaces
9 interfaces between chains.
- B–A · 2197 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2136 Ų buried · 18 hydrogen bonds · protein-protein
- D–R · 501 Ų buried · 7 hydrogen bonds · protein-protein
- P–A · 478 Ų buried · 6 hydrogen bonds · protein-protein
- P–B · 315 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7RLZ · Antibody 2F2 in complex with P. vivax CSP peptide GDRAAGQPAGNGAGGQAA · 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 P against A, TM-score 0.37
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 7RLZ · PDBe 7RLZ · UniProt P08677
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