MolNFT v1 · #186682 · protein
Antibody 2E10.E9 in complex with P. vivax csp peptide angagnqpgangagnqpgangaggqaa
7RM3 · 2E10.E9 Fab heavy chain: “Antibody 2E10.E9 in complex with P. vivax csp peptide angagnqpgangagnqpgangaggqaa”. X-ray diffraction, 1 ligand (NA), 8 pockets (best druggability 0.82). MolNFT v1 #186682 on GenesisL1: 3D structure…
- PDB
- 7RM3
- Type
- protein
- Length
- 903 residues
- Chains
- 6
- 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
- B7SA67
- Ligands
- NA
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2E10.E9 Fab heavy chain | protein | 221 | 8% helix, 52% strand | — |
| B, D | 2E10.E9 Fab light chain | protein | 219 | 6% helix, 48% strand | — |
| C | 2E10.E9 Fab heavy chain | protein | 222 | 8% helix, 51% strand | — |
| P | Peptide from circumsporozoite protein variant VK247 | protein | 12 | 0% helix, 0% strand | B7SA67 |
| Q | Peptide from circumsporozoite protein variant VK247 | protein | 10 | 0% helix, 0% strand | B7SA67 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.82 | 0.83 | 107 | empty |
| 2 | 497 | 0.66 | 0.78 | 45 | empty |
| 3 | 241 | 0.65 | 0.83 | 39 | ACT |
| 4 | 364 | 0.61 | 0.78 | 41 | empty |
| 5 | 254 | 0.54 | 0.76 | 48 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2040 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1948 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 669 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 468 Ų buried · 8 hydrogen bonds · protein-protein
- C–P · 340 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 7RM3 · Antibody 2E10.E9 in complex with P. vivax CSP peptide ANGAGNQPGANGAGNQPGANGAGGQAA · 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 B7SA67
- Elsewhere: RCSB PDB 7RM3 · PDBe 7RM3 · UniProt B7SA67
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