Research workbench
Structure of MERS-cov rbd in complex with a fully human antibody MCA1
Analyse Structure of MERS-cov rbd in complex with a fully human antibody MCA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GMQ
- Type
- protein
- Length
- 639 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S protein; MCA1 heavy chain; MCA1 light chain
- UniProt
- V5RDT9
- Ligands
- MAN, NAG
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S protein | protein | 205 | 15% helix, 35% strand | V5RDT9 |
| B | MCA1 heavy chain | protein | 225 | 6% helix, 48% strand | — |
| C | MCA1 light chain | protein | 209 | 7% helix, 45% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.55 | 0.74 | 43 | empty |
| 2 | 91 | 0.48 | 0.81 | 21 | empty |
| 3 | 75 | 0.32 | 0.74 | 17 | EDO |
| 4 | 69 | 0.30 | 0.74 | 19 | empty |
| 5 | 58 | 0.28 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1891 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 872 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5GMQ · Structure of MERS-CoV RBD in complex with a fully human antibody MCA1 · 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 V5RDT9
- Elsewhere: RCSB PDB 5GMQ · PDBe 5GMQ · UniProt V5RDT9
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