MolNFT v1 · #186674 · protein
Antibody 2F2 in complex with P. vivax csp peptide gdradgqpagdradgqpa
7RLV · 2F2 Fab light chain: “Antibody 2F2 in complex with P. vivax csp peptide gdradgqpagdradgqpa”. X-ray diffraction, 10 pockets (best druggability 0.65). MolNFT v1 #186674 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RLV
- Type
- protein
- Length
- 1,332 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2F2 Fab light chain; Peptide from circumsporozoite protein variant VK210; 2F2 Fab heavy…
- UniProt
- P08677
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 8 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 2F2 Fab light chain | protein | 219 | 6% helix, 51% strand | — |
| P, R | Peptide from circumsporozoite protein variant VK210 | protein | 12 | 25% helix, 0% strand | P08677 |
| A | 2F2 Fab heavy chain | protein | 213 | 8% helix, 55% strand | — |
| D | 2F2 Fab light chain | protein | 218 | 6% helix, 52% strand | — |
| C | 2F2 Fab heavy chain | protein | 209 | 9% helix, 55% strand | — |
| F | 2F2 Fab light chain | protein | 216 | 6% helix, 52% strand | — |
| Q | Peptide from circumsporozoite protein variant VK210 | protein | 14 | 21% helix, 0% strand | P08677 |
| E | 2F2 Fab heavy chain | protein | 219 | 8% helix, 55% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.65 | 0.73 | 95 | empty |
| 2 | 585 | 0.62 | 0.74 | 68 | empty |
| 3 | 385 | 0.60 | 0.76 | 38 | empty |
| 4 | 425 | 0.57 | 0.74 | 51 | empty |
| 5 | 408 | 0.55 | 0.73 | 37 | empty |
Interfaces
14 interfaces between chains.
- F–E · 1983 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 1867 Ų buried · 14 hydrogen bonds · protein-protein
- D–C · 1864 Ų buried · 17 hydrogen bonds · protein-protein
- R–C · 536 Ų buried · 7 hydrogen bonds · protein-protein
- Q–E · 519 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7RLV · Antibody 2F2 in complex with P. vivax CSP peptide GDRADGQPAGDRADGQPA · the same entry in another collection · chain E against E, 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 0.32
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 7RLV · PDBe 7RLV · UniProt P08677
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