Research workbench
Unusual twinning in crystals of the cits binding antibody Fab fragment F3P4
Analyse Unusual twinning in crystals of the cits binding antibody Fab fragment F3P4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V7N
- Type
- protein
- Length
- 1,700 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin light chain; Immunoglobulin heavy chain
- Pockets
- 19 · best druggability 0.66
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Immunoglobulin light chain | protein | 213 | 7% helix, 51% strand | — |
| B | Immunoglobulin heavy chain | protein | 214 | 10% helix, 52% strand | — |
| C, G | Immunoglobulin light chain | protein | 212 | 7% helix, 50% strand | — |
| D | Immunoglobulin heavy chain | protein | 213 | 8% helix, 53% strand | — |
| F | Immunoglobulin heavy chain | protein | 212 | 10% helix, 52% strand | — |
| H | Immunoglobulin heavy chain | protein | 211 | 10% helix, 53% strand | — |
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.66 | 0.76 | 49 | empty |
| 2 | 60 | 0.56 | 0.89 | 21 | empty |
| 3 | 384 | 0.56 | 0.74 | 34 | empty |
| 4 | 334 | 0.53 | 0.74 | 50 | empty |
| 5 | 330 | 0.53 | 0.74 | 32 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1647 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1637 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1614 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1613 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 275 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 2V7N · Unusual twinning in crystals of the CitS binding antibody Fab fragment f3p4 · 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
- Elsewhere: RCSB PDB 2V7N · PDBe 2V7N
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