MolNFT v1 · #169063 · protein
LY3041658 Fab bound to CXCL7
6WZL · LY3041658 Fab heavy chain: “LY3041658 Fab bound to CXCL7”. X-ray diffraction, 13 pockets (best druggability 0.59). MolNFT v1 #169063 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WZL
- Type
- protein
- Length
- 996 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 7
- UniProt
- A0A2K5UVV0
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LY3041658 Fab heavy chain | protein | 220 | 8% helix, 50% strand | — |
| B, D | LY3041658 Fab light chain | protein | 213 | 6% helix, 49% strand | — |
| C | LY3041658 Fab heavy chain | protein | 223 | 9% helix, 48% strand | — |
| E | C-X-C motif chemokine 7 | protein | 64 | 22% helix, 28% strand | A0A2K5UVV0 |
| F | C-X-C motif chemokine 7 | protein | 63 | 24% helix, 32% strand | A0A2K5UVV0 |
Ligands and binding sites
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.59 | 0.74 | 53 | empty |
| 2 | 396 | 0.57 | 0.74 | 49 | PG6 |
| 3 | 189 | 0.51 | 0.77 | 33 | empty |
| 4 | 71 | 0.51 | 0.85 | 20 | empty |
| 5 | 63 | 0.50 | 0.86 | 24 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1911 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1867 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 882 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 882 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 880 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 6WZL · LY3041658 Fab bound to CXCL7 · 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 A0A2K5UVV0
- Elsewhere: RCSB PDB 6WZL · PDBe 6WZL · UniProt A0A2K5UVV0
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