MolNFT v1 · #99900 · protein
Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/GOOSE/GUANGDONG/1/96 (H5N1)
4MHJ · Hemagglutinin HA1 chain: “Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from A/GOOSE/GUANGDONG/1/96 (H5N1)”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4MHJ
- Type
- protein
- Length
- 5,569 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; H5M9 antibody, light chain (kappa)…
- UniProt
- Q9Q0U6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 16 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M, S | Hemagglutinin HA1 chain | protein | 322 | 10% helix, 40% strand | Q9Q0U6 |
| B, D, P | Hemagglutinin HA2 chain | protein | 172 | 56% helix, 10% strand | Q9Q0U6 |
| C | Hemagglutinin HA1 chain | protein | 321 | 10% helix, 39% strand | Q9Q0U6 |
| G | Hemagglutinin HA1 chain | protein | 321 | 10% helix, 38% strand | Q9Q0U6 |
| N | Hemagglutinin HA2 chain | protein | 169 | 57% helix, 7% strand | Q9Q0U6 |
| O | Hemagglutinin HA1 chain | protein | 318 | 10% helix, 40% strand | Q9Q0U6 |
| L | H5M9 antibody, light chain (kappa) | protein | 215 | 5% helix, 47% strand | — |
| E, X | H5M9 antibody, light chain (kappa) | protein | 216 | 5% helix, 47% strand | — |
| J | H5M9 antibody, light chain (kappa) | protein | 211 | 5% helix, 46% strand | — |
| Q | H5M9 antibody, light chain (kappa) | protein | 215 | 5% helix, 47% strand | — |
| V | H5M9 antibody, light chain (kappa) | protein | 214 | 5% helix, 46% strand | — |
| I, U | Hemagglutinin HA2 chain | protein | 173 | 56% helix, 13% strand | Q9Q0U6 |
| H, R | H5M9 antibody, heavy chain (IGG1) | protein | 221 | 5% helix, 49% strand | — |
| F, W | H5M9 antibody, heavy chain (IGG1) | protein | 221 | 5% helix, 48% strand | — |
| K | H5M9 antibody, heavy chain (IGG1) | protein | 221 | 7% helix, 48% strand | — |
| T | H5M9 antibody, heavy chain (IGG1) | protein | 220 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, G, C, M, S, O, P
- MAN · alpha-D-mannopyranose · sugar · 9 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 390 | 0.83 | 0.92 | 77 | empty |
| 2 | 488 | 0.82 | 0.89 | 67 | empty |
| 3 | 397 | 0.81 | 0.90 | 56 | empty |
| 4 | 297 | 0.81 | 0.92 | 61 | empty |
| 5 | 66 | 0.75 | 0.99 | 15 | empty |
Interfaces
54 interfaces between chains.
- S–U · 2554 Ų buried · 44 hydrogen bonds · protein-protein
- G–I · 2477 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2434 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2380 Ų buried · 28 hydrogen bonds · protein-protein
- M–N · 2324 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 4MHJ · Crystal structure of Fab H5M9 in complex with influenza virus hemagglutinin from… · the same entry in another collection · chain E against E, 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 Q9Q0U6
- Elsewhere: RCSB PDB 4MHJ · PDBe 4MHJ · UniProt Q9Q0U6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.