MolNFT v1 · #186680 · protein
Antibody 2F2 in complex with P. vivax csp peptide edgagnqpgangagnqpgangagnqpg
7RM1 · 2E10.E9 Fab heavy chain: “Antibody 2F2 in complex with P. vivax csp peptide edgagnqpgangagnqpgangagnqpg”. X-ray diffraction, 9 pockets (best druggability 0.58). MolNFT v1 #186680 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7RM1
- Type
- protein
- Length
- 898 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2E10.E9 Fab heavy chain; 2E10.E9 Fab light chain; Peptide from circumsporozoite protein…
- UniProt
- B7SA68
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 2E10.E9 Fab heavy chain | protein | 221 | 8% helix, 51% strand | — |
| B, D | 2E10.E9 Fab light chain | protein | 219 | 4% helix, 49% strand | — |
| P | Peptide from circumsporozoite protein variant VK247 | protein | 18 | 0% helix, 11% strand | B7SA68 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.58 | 0.74 | 51 | empty |
| 2 | 449 | 0.57 | 0.73 | 50 | empty |
| 3 | 221 | 0.51 | 0.76 | 28 | empty |
| 4 | 174 | 0.50 | 0.77 | 34 | empty |
| 5 | 116 | 0.40 | 0.75 | 18 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1894 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1882 Ų buried · 15 hydrogen bonds · protein-protein
- A–P · 424 Ų buried · 8 hydrogen bonds · protein-protein
- C–P · 323 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 304 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7RM1 · Antibody 2F2 in complex with P. vivax CSP peptide EDGAGNQPGANGAGNQPGANGAGNQPG · the same entry in another collection · chain A against A, TM-score 1.00
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 B7SA68
- Elsewhere: RCSB PDB 7RM1 · PDBe 7RM1 · UniProt B7SA68
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