Research workbench
Complex structure of MERS-rbd bound with 4C2 antibody
Analyse Complex structure of MERS-rbd bound with 4C2 antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DO2
- Type
- protein
- Length
- 1,274 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S protein; 4C2 heavy chain; 4C2 light chain
- UniProt
- W5ZZM0
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | S protein | protein | 208 | 16% helix, 37% strand | W5ZZM0 |
| H, C | 4C2 heavy chain | protein | 215 | 4% helix, 52% strand | — |
| L, D | 4C2 light chain | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.87 | 0.88 | 123 | empty |
| 2 | 880 | 0.76 | 0.79 | 90 | empty |
| 3 | 907 | 0.75 | 0.79 | 123 | empty |
| 4 | 66 | 0.75 | 0.98 | 15 | empty |
| 5 | 217 | 0.60 | 0.81 | 29 | empty |
Interfaces
11 interfaces between chains.
- H–L · 1901 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1867 Ų buried · 18 hydrogen bonds · protein-protein
- L–B · 799 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 717 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 660 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5DO2 · Complex structure of MERS-RBD bound with 4C2 antibody · 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 W5ZZM0
- Elsewhere: RCSB PDB 5DO2 · PDBe 5DO2 · UniProt W5ZZM0
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