MolNFT v1 · #144864 · protein
Crystal structure of potent neutralizing antibody CDC2-C2 in complex with MERS-cov S1 rbd
6C6Z · Spike protein: “Crystal structure of potent neutralizing antibody CDC2-C2 in complex with MERS-cov S1 rbd”. X-ray diffraction, 1 ligand (NAG), 13 pockets (best druggability 0.63). MolNFT v1 #144864 on GenesisL1: 3D structure…
- PDB
- 6C6Z
- Type
- protein
- Length
- 1,251 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein; Antibody CDC2-C2 heavy chain; Antibody CDC2-C2 light chain
- UniProt
- A0A0U2MS80
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein | protein | 187 | 15% helix, 37% strand | A0A0U2MS80 |
| B | Spike protein | protein | 188 | 16% helix, 37% strand | A0A0U2MS80 |
| C | Antibody CDC2-C2 heavy chain | protein | 222 | 10% helix, 52% strand | — |
| D, L | Antibody CDC2-C2 light chain | protein | 215 | 5% helix, 53% strand | — |
| H | Antibody CDC2-C2 heavy chain | protein | 224 | 9% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.63 | 0.93 | 21 | empty |
| 2 | 368 | 0.57 | 0.75 | 44 | empty |
| 3 | 162 | 0.55 | 0.81 | 23 | empty |
| 4 | 334 | 0.52 | 0.73 | 44 | empty |
| 5 | 56 | 0.49 | 0.86 | 21 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1779 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1743 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 837 Ų buried · 15 hydrogen bonds · protein-protein
- B–H · 832 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 490 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6C6Z · Crystal structure of potent neutralizing antibody CDC2-C2 in complex with MERS-CoV S1 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 A0A0U2MS80
- Elsewhere: RCSB PDB 6C6Z · PDBe 6C6Z · UniProt A0A0U2MS80
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