MolNFT v1 · #123811 · protein
Structure of MEDI8852 Fab fragment in complex with H5 ha
5JW4 · Hemagglutinin: “Structure of MEDI8852 Fab fragment in complex with H5 ha”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #123811 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JW4
- Type
- protein
- Length
- 5,368 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; MEDI8852 heavy chain; MEDI8852 light chain
- UniProt
- Q6DQ34
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin | protein | 321 | 9% helix, 40% strand | Q6DQ34 |
| B, D, F, H, J, L | Hemagglutinin | protein | 162 | 51% helix, 14% strand | Q6DQ34 |
| M, O, S, U, W | MEDI8852 heavy chain | protein | 223 | 6% helix, 53% strand | — |
| N, P, T, V, X | MEDI8852 light chain | protein | 206 | 7% helix, 52% strand | — |
| Q | MEDI8852 heavy chain | protein | 177 | 3% helix, 50% strand | — |
| R | MEDI8852 light chain | protein | 148 | 2% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains B, E, F, H, J, A, C, D, G, I, K, 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 | 1015 | 0.88 | 0.89 | 143 | empty |
| 2 | 506 | 0.83 | 0.90 | 85 | empty |
| 3 | 426 | 0.81 | 0.89 | 61 | empty |
| 4 | 78 | 0.77 | 0.99 | 16 | empty |
| 5 | 80 | 0.77 | 0.99 | 15 | empty |
Interfaces
56 interfaces between chains.
- E–F · 2483 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 2467 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 2443 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2441 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2440 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 59 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 5JW4 · Structure of MEDI8852 Fab Fragment in Complex with H5 HA · the same entry in another collection · chain B against B, 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 Q6DQ34
- Elsewhere: RCSB PDB 5JW4 · PDBe 5JW4 · UniProt Q6DQ34
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