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PFS230 D1 domain in complex with neutralizing antibody LMIV230-01
Analyse PFS230 D1 domain in complex with neutralizing antibody LMIV230-01 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JUM
- Type
- protein
- Length
- 1,207 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gametocyte surface protein P230; Neutralizing antibody, LMIV230-01 single-chain fv
- UniProt
- P68874
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gametocyte surface protein P230 | protein | 176 | 6% helix, 43% strand | P68874 |
| B | Gametocyte surface protein P230 | protein | 174 | 6% helix, 43% strand | P68874 |
| C | Gametocyte surface protein P230 | protein | 172 | 6% helix, 44% strand | P68874 |
| H | Neutralizing antibody, LMIV230-01 single-chain fv | protein | 228 | 7% helix, 50% strand | — |
| I | Neutralizing antibody, LMIV230-01 single-chain fv | protein | 230 | 7% helix, 49% strand | — |
| J | Neutralizing antibody, LMIV230-01 single-chain fv | protein | 227 | 7% helix, 50% strand | — |
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.81 | 0.83 | 108 | empty |
| 2 | 534 | 0.77 | 0.84 | 50 | empty |
| 3 | 472 | 0.73 | 0.83 | 65 | empty |
| 4 | 188 | 0.51 | 0.77 | 26 | empty |
| 5 | 162 | 0.50 | 0.78 | 35 | empty |
Interfaces
9 interfaces between chains.
- B–I · 1081 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 1040 Ų buried · 19 hydrogen bonds · protein-protein
- C–J · 1039 Ų buried · 18 hydrogen bonds · protein-protein
- A–I · 445 Ų buried · 5 hydrogen bonds · protein-protein
- B–H · 430 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7JUM · Pfs230 D1 domain in complex with neutralizing antibody LMIV230-01 · 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 P68874
- Elsewhere: RCSB PDB 7JUM · PDBe 7JUM · UniProt P68874
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