MolNFT v1 · #109699 · protein
Crystal structure of potent neutralizing antibody M336 in complex with MERS co-V rbd
4XAK · Spike glycoprotein: “Crystal structure of potent neutralizing antibody M336 in complex with MERS co-V rbd”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.57). MolNFT v1 #109699 on GenesisL1: 3D structure…
- PDB
- 4XAK
- Type
- protein
- Length
- 1,286 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of neutralizing antibody M336; Light chain of…
- UniProt
- K9N5Q8
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 211 | 16% helix, 35% strand | K9N5Q8 |
| H | Heavy chain of neutralizing antibody M336 | protein | 227 | 7% helix, 52% strand | — |
| L | Light chain of neutralizing antibody M336 | protein | 212 | 6% helix, 50% strand | — |
| D | Heavy chain of neutralizing antibody M336 | protein | 218 | 6% helix, 52% strand | — |
| E | Light chain of neutralizing antibody M336 | protein | 207 | 4% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.57 | 0.75 | 37 | empty |
| 2 | 355 | 0.55 | 0.74 | 38 | empty |
| 3 | 122 | 0.55 | 0.83 | 23 | empty |
| 4 | 87 | 0.41 | 0.79 | 20 | empty |
| 5 | 105 | 0.39 | 0.76 | 24 | empty |
Interfaces
7 interfaces between chains.
- H–L · 2069 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1951 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 809 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 769 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 134 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4XAK · Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD · 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 K9N5Q8
- Elsewhere: RCSB PDB 4XAK · PDBe 4XAK · UniProt K9N5Q8
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