MolNFT v1 · #169062 · protein
LY3041658 Fab bound to CXCL3
6WZK · LY3041658 Fab heavy chain: “LY3041658 Fab bound to CXCL3”. X-ray diffraction, 1 ligand (MG), 11 pockets (best druggability 0.60). MolNFT v1 #169062 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WZK
- Type
- protein
- Length
- 998 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 3
- UniProt
- Q0EAC1
- Ligands
- MG
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LY3041658 Fab heavy chain | protein | 222 | 8% helix, 50% strand | — |
| B, D | LY3041658 Fab light chain | protein | 214 | 7% helix, 50% strand | — |
| C | LY3041658 Fab heavy chain | protein | 220 | 8% helix, 51% strand | — |
| E, F | C-X-C motif chemokine 3 | protein | 64 | 22% helix, 31% strand | Q0EAC1 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.60 | 0.74 | 54 | empty |
| 2 | 383 | 0.57 | 0.75 | 48 | empty |
| 3 | 70 | 0.57 | 0.89 | 21 | empty |
| 4 | 205 | 0.52 | 0.77 | 34 | empty |
| 5 | 59 | 0.49 | 0.86 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1918 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1914 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 884 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 859 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 816 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 6WZK · LY3041658 Fab bound to CXCL3 · 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 Q0EAC1
- Elsewhere: RCSB PDB 6WZK · PDBe 6WZK · UniProt Q0EAC1
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