Research workbench
Inferred precursor (uca) of the human antibody lineage K03.12 in complex with influenza hemagglutinin H1 solomon ISLANDS/03/2006
Analyse Inferred precursor (uca) of the human antibody lineage K03.12 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W0D
- Type
- protein
- Length
- 651 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Lineage K03.12 uca antibody heavy chain; Lineage K03.12 uca antibody…
- UniProt
- D1MPH2, S6B2A6, Q6IPQ0
- Ligands
- NAG, BMA
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 214 | 12% helix, 40% strand | D1MPH2 |
| B | Lineage K03.12 uca antibody heavy chain | protein | 235 | 9% helix, 49% strand | S6B2A6 |
| C | Lineage K03.12 uca antibody light chain | protein | 202 | 6% helix, 51% strand | Q6IPQ0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.63 | 0.78 | 54 | empty |
| 2 | 468 | 0.58 | 0.74 | 56 | GOL |
| 3 | 159 | 0.57 | 0.81 | 20 | empty |
| 4 | 89 | 0.36 | 0.75 | 23 | empty |
| 5 | 64 | 0.31 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1884 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 572 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 79 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5W0D · Inferred precursor (UCA) of the human antibody lineage K03.12 in complex with influenza… · 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 D1MPH2
- Every structure of UniProt S6B2A6
- Every structure of UniProt Q6IPQ0
- Elsewhere: RCSB PDB 5W0D · PDBe 5W0D · UniProt D1MPH2 · UniProt S6B2A6 · UniProt Q6IPQ0
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