MolNFT v1 · #186677 · protein
Antibody 2F2 in complex with P. vivax csp peptide draagqpagdradgqpa
7RLY · Peptide from circumsporozoite protein variant VK210: “Antibody 2F2 in complex with P. vivax csp peptide draagqpagdradgqpa”. X-ray diffraction, 13 pockets (best druggability 0.65). MolNFT v1 #186677 on GenesisL1: 3D structure…
- PDB
- 7RLY
- Type
- protein
- Length
- 1,360 residues
- Chains
- 9
- 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
- 13 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Peptide from circumsporozoite protein variant VK210 | protein | 15 | 20% helix, 0% strand | P08677 |
| B, D, F | 2F2 Fab light chain | protein | 218 | 7% helix, 50% strand | — |
| A, C | 2F2 Fab heavy chain | protein | 221 | 10% helix, 53% strand | — |
| E | 2F2 Fab heavy chain | protein | 220 | 10% helix, 54% strand | — |
| R | Peptide from circumsporozoite protein variant VK210 | protein | 16 | 19% helix, 0% strand | P08677 |
| Q | Peptide from circumsporozoite protein variant VK210 | protein | 13 | 23% helix, 0% strand | P08677 |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.65 | 0.76 | 77 | empty |
| 2 | 580 | 0.61 | 0.74 | 61 | empty |
| 3 | 390 | 0.60 | 0.76 | 40 | empty |
| 4 | 501 | 0.58 | 0.73 | 70 | empty |
| 5 | 165 | 0.52 | 0.79 | 26 | empty |
Interfaces
14 interfaces between chains.
- B–A · 2087 Ų buried · 19 hydrogen bonds · protein-protein
- D–C · 2084 Ų buried · 21 hydrogen bonds · protein-protein
- F–E · 2060 Ų buried · 17 hydrogen bonds · protein-protein
- E–R · 532 Ų buried · 4 hydrogen bonds · protein-protein
- P–C · 527 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7RLY · Antibody 2F2 in complex with P. vivax CSP peptide DRAAGQPAGDRADGQPA · the same entry in another collection · chain F against F, 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 0.32
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 7RLY · PDBe 7RLY · UniProt P08677
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