MolNFT v1 · #107473 · protein
Crystal structure of a neutralizing human monoclonal antibody with 1968 H3 ha
4UBD · Hemagglutinin HA1 chain: “Crystal structure of a neutralizing human monoclonal antibody with 1968 H3 ha”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.88). MolNFT v1 #107473 on GenesisL1: 3D…
- PDB
- 4UBD
- Type
- protein
- Length
- 5,494 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Monoclonal antibody H chain; Monoclonal…
- UniProt
- Q91MA7
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 9 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, U, M, Q, E | Hemagglutinin HA1 chain | protein | 320 | 9% helix, 38% strand | Q91MA7 |
| V | Hemagglutinin HA2 chain | protein | 164 | 57% helix, 13% strand | Q91MA7 |
| I | Hemagglutinin HA1 chain | protein | 317 | 10% helix, 38% strand | Q91MA7 |
| F, N | Hemagglutinin HA2 chain | protein | 163 | 57% helix, 14% strand | Q91MA7 |
| B | Hemagglutinin HA2 chain | protein | 165 | 55% helix, 13% strand | Q91MA7 |
| J | Hemagglutinin HA2 chain | protein | 164 | 57% helix, 14% strand | Q91MA7 |
| R | Hemagglutinin HA2 chain | protein | 166 | 54% helix, 13% strand | Q91MA7 |
| C, Y, G, S, O, K | Monoclonal antibody H chain | protein | 219 | 4% helix, 47% strand | — |
| D, X, H, T, P, L | Monoclonal antibody L chain | protein | 213 | 8% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, I, C, U, M, E, Q, S, B, V, K, N, R
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains I, M, E, U, A
- MAN · alpha-D-mannopyranose · sugar · 6 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 | 934 | 0.88 | 0.90 | 130 | empty |
| 2 | 939 | 0.86 | 0.87 | 97 | empty |
| 3 | 562 | 0.83 | 0.88 | 44 | empty |
| 4 | 631 | 0.82 | 0.87 | 51 | empty |
| 5 | 982 | 0.78 | 0.80 | 79 | empty |
Interfaces
72 interfaces between chains.
- A–B · 3017 Ų buried · 44 hydrogen bonds · protein-protein
- U–V · 3007 Ų buried · 39 hydrogen bonds · protein-protein
- Q–R · 3003 Ų buried · 42 hydrogen bonds · protein-protein
- M–N · 2968 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2963 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 4UBD · Crystal structure of a neutralizing human monoclonal antibody with 1968 H3 HA · 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 Q91MA7
- Elsewhere: RCSB PDB 4UBD · PDBe 4UBD · UniProt Q91MA7
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