MolNFT v1 · #169061 · protein
LY3041658 Fab bound to CXCL2
6WZJ · LY3041658 Fab heavy chain: “LY3041658 Fab bound to CXCL2”. X-ray diffraction, 12 pockets (best druggability 0.62). MolNFT v1 #169061 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WZJ
- Type
- protein
- Length
- 991 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LY3041658 Fab heavy chain; LY3041658 Fab light chain; C-X-C motif chemokine 2
- UniProt
- Q0EAC2
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LY3041658 Fab heavy chain | protein | 221 | 5% helix, 50% strand | — |
| B, D | LY3041658 Fab light chain | protein | 213 | 7% helix, 50% strand | — |
| C | LY3041658 Fab heavy chain | protein | 222 | 5% helix, 50% strand | — |
| E | C-X-C motif chemokine 2 | protein | 63 | 16% helix, 30% strand | Q0EAC2 |
| F | C-X-C motif chemokine 2 | protein | 59 | 15% helix, 31% strand | Q0EAC2 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.62 | 0.77 | 48 | empty |
| 2 | 348 | 0.55 | 0.74 | 50 | empty |
| 3 | 300 | 0.52 | 0.74 | 50 | empty |
| 4 | 53 | 0.49 | 0.87 | 23 | empty |
| 5 | 125 | 0.47 | 0.78 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1907 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1884 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 773 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 752 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 713 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6WZJ · LY3041658 Fab bound to CXCL2 · 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 Q0EAC2
- Elsewhere: RCSB PDB 6WZJ · PDBe 6WZJ · UniProt Q0EAC2
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