MolNFT v1 · #148079 · protein
Crystal structure of GII.4 unsw 2012 P domain in complex with Fab 10E9
6EWB · VP1: “Crystal structure of GII.4 unsw 2012 P domain in complex with Fab 10E9”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #148079 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EWB
- Type
- protein
- Length
- 2,890 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; Fab heavy chain; Fab light chain
- UniProt
- K4LM89
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 12 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 307 | 5% helix, 36% strand | K4LM89 |
| B | VP1 | protein | 306 | 6% helix, 35% strand | K4LM89 |
| C | VP1 | protein | 310 | 5% helix, 35% strand | K4LM89 |
| D | VP1 | protein | 309 | 5% helix, 35% strand | K4LM89 |
| E | Fab heavy chain | protein | 195 | 8% helix, 54% strand | — |
| F | Fab light chain | protein | 209 | 3% helix, 54% strand | — |
| G | Fab heavy chain | protein | 211 | 9% helix, 54% strand | — |
| H | Fab heavy chain | protein | 210 | 7% helix, 52% strand | — |
| I | Fab light chain | protein | 211 | 5% helix, 53% strand | — |
| J | Fab heavy chain | protein | 207 | 9% helix, 52% strand | — |
| K | Fab light chain | protein | 205 | 3% helix, 52% strand | — |
| L | Fab light chain | protein | 210 | 5% helix, 52% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.77 | 0.85 | 63 | empty |
| 2 | 176 | 0.77 | 0.93 | 29 | empty |
| 3 | 178 | 0.76 | 0.92 | 35 | empty |
| 4 | 171 | 0.76 | 0.92 | 31 | empty |
| 5 | 199 | 0.76 | 0.91 | 36 | empty |
Interfaces
24 interfaces between chains.
- A–B · 1750 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1715 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1686 Ų buried · 18 hydrogen bonds · protein-protein
- J–K · 1662 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 1658 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6EWB · Crystal structure of GII.4 UNSW 2012 P domain in complex with Fab 10E9 · 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 K4LM89
- Elsewhere: RCSB PDB 6EWB · PDBe 6EWB · UniProt K4LM89
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.