Research workbench
Crystal structure of human Fab H5.28 in complex with influenza a H5N1 vietnam hemagglutinin head domain
Analyse Crystal structure of human Fab H5.28 in complex with influenza a H5N1 vietnam… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P3S
- Type
- protein
- Length
- 4,991 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human Fab H5.28 heavy chain; Human Fab H5.28 light chain; Hemagglutinin
- UniProt
- Q1KHK2
- Ligands
- NAG, MAN, SIA, BMA, NDG, GAL, GLA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 23 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human Fab H5.28 heavy chain | protein | 225 | 4% helix, 45% strand | — |
| B | Human Fab H5.28 light chain | protein | 215 | 6% helix, 48% strand | — |
| C | Human Fab H5.28 heavy chain | protein | 218 | 4% helix, 48% strand | — |
| D | Human Fab H5.28 light chain | protein | 203 | 6% helix, 46% strand | — |
| E | Hemagglutinin | protein | 196 | 12% helix, 33% strand | Q1KHK2 |
| F | Human Fab H5.28 heavy chain | protein | 223 | 3% helix, 49% strand | — |
| G, N | Human Fab H5.28 light chain | protein | 214 | 1% helix, 47% strand | — |
| H | Hemagglutinin | protein | 202 | 12% helix, 34% strand | Q1KHK2 |
| I | Human Fab H5.28 heavy chain | protein | 217 | 4% helix, 45% strand | — |
| J | Human Fab H5.28 light chain | protein | 187 | 4% helix, 37% strand | — |
| K | Hemagglutinin | protein | 206 | 10% helix, 35% strand | Q1KHK2 |
| L | Hemagglutinin | protein | 185 | 11% helix, 35% strand | Q1KHK2 |
| M | Human Fab H5.28 heavy chain | protein | 225 | 3% helix, 48% strand | — |
| O | Hemagglutinin | protein | 209 | 11% helix, 35% strand | Q1KHK2 |
| P | Human Fab H5.28 heavy chain | protein | 220 | 4% helix, 45% strand | — |
| Q | Human Fab H5.28 light chain | protein | 202 | 7% helix, 37% strand | — |
| R | Hemagglutinin | protein | 194 | 9% helix, 31% strand | Q1KHK2 |
| S | Human Fab H5.28 heavy chain | protein | 224 | 4% helix, 46% strand | — |
| T | Human Fab H5.28 light chain | protein | 214 | 6% helix, 42% strand | — |
| U | Hemagglutinin | protein | 196 | 13% helix, 34% strand | Q1KHK2 |
| V | Human Fab H5.28 heavy chain | protein | 208 | 4% helix, 44% strand | — |
| W | Human Fab H5.28 light chain | protein | 198 | 6% helix, 43% strand | — |
| X | Hemagglutinin | protein | 196 | 10% helix, 29% strand | Q1KHK2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains E, H, K, O, X, L, R, U
- MAN · alpha-D-mannopyranose · sugar · 9 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 8 copies · chains U, H
- BMA · beta-D-mannopyranose · sugar · 7 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 6 copies
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains U
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains H
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 | 1074 | 0.78 | 0.80 | 98 | empty |
| 2 | 371 | 0.77 | 0.87 | 65 | empty |
| 3 | 826 | 0.77 | 0.80 | 137 | empty |
| 4 | 831 | 0.75 | 0.79 | 105 | empty |
| 5 | 1060 | 0.74 | 0.77 | 126 | empty |
Interfaces
38 interfaces between chains.
- A–B · 1784 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 1594 Ų buried · 8 hydrogen bonds · protein-protein
- M–N · 1519 Ų buried · 12 hydrogen bonds · protein-protein
- S–T · 1488 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 1424 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 9 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6P3S · Crystal structure of human Fab H5.28 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 6P3S · PDBe 6P3S · UniProt Q1KHK2
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