MolNFT v1 · #159867 · protein
Crystal structure of human Fab H5.31 in complex with influenza a H5N1 vietnam hemagglutinin head domain
6P3R · Human Fab H5.31 heavy chain: “Crystal structure of human Fab H5.31 in complex with influenza a H5N1 vietnam hemagglutinin head domain”. X-ray diffraction, 9 ligands (NAG, NDG, MAN), 19 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 6P3R
- Type
- protein
- Length
- 1,294 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human Fab H5.31 heavy chain; Human Fab H5.31 light chain; Hemagglutinin
- UniProt
- Q1KHK2
- Ligands
- NAG, NDG, MAN, SIA, BMA, GLA, GAL, Z9N, PO4
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human Fab H5.31 heavy chain | protein | 224 | 7% helix, 56% strand | — |
| B, D | Human Fab H5.31 light chain | protein | 215 | 5% helix, 52% strand | — |
| C | Human Fab H5.31 heavy chain | protein | 230 | 7% helix, 55% strand | — |
| E | Hemagglutinin | protein | 202 | 10% helix, 36% strand | Q1KHK2 |
| L | Hemagglutinin | protein | 208 | 12% helix, 38% strand | Q1KHK2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, E, L, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GLA · alpha-D-galactopyranose · sugar
- GAL · beta-D-galactopyranose · sugar
- Z9N · alpha-D-fructofuranose · sugar · chains L
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, L, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.71 | 0.77 | 83 | empty |
| 2 | 606 | 0.63 | 0.74 | 64 | empty |
| 3 | 269 | 0.62 | 0.80 | 48 | empty |
| 4 | 63 | 0.60 | 0.90 | 18 | empty |
| 5 | 301 | 0.53 | 0.75 | 31 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2152 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2049 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 874 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 685 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 685 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6P3R · crystal structure of human Fab H5.31 in complex with influenza A H5N1 Vietnam… · 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 Q1KHK2
- Elsewhere: RCSB PDB 6P3R · PDBe 6P3R · UniProt Q1KHK2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.