MolNFT v1 · #51441 · protein
Unusual twinning in crystals of the cits binding antibody Fab fragment F3P4
2V7N · Immunoglobulin light chain: “Unusual twinning in crystals of the cits binding antibody Fab fragment F3P4”. X-ray diffraction, 19 pockets (best druggability 0.66). MolNFT v1 #51441 on GenesisL1: 3D structure, binding sites and…
- 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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