MolNFT v1 · #160894 · protein
Crystal structure of MERS-cov S1-ntd bound with G2 Fab
6PXH: “Crystal structure of MERS-cov S1-ntd bound with G2 Fab”. X-ray diffraction, 5 ligands (DHF, NAG, MAN), 20 pockets (best druggability 0.73). MolNFT v1 #160894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PXH
- Type
- protein
- Length
- 1,538 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MERS-cov S1-ntd; G2 heavy chain; G2 light chain
- UniProt
- V9TWK2
- Ligands
- DHF, NAG, MAN, BMA, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MERS-cov S1-ntd | protein | 334 | 11% helix, 40% strand | V9TWK2 |
| B | MERS-cov S1-ntd | protein | 341 | 10% helix, 40% strand | V9TWK2 |
| C | G2 heavy chain | protein | 213 | 7% helix, 55% strand | — |
| D | G2 light chain | protein | 218 | 6% helix, 52% strand | — |
| H | G2 heavy chain | protein | 220 | 8% helix, 55% strand | — |
| L | G2 light chain | protein | 212 | 5% helix, 53% strand | — |
Ligands and binding sites
- DHF · Dihydrofolic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.73 | 0.97 | 18 | empty |
| 2 | 88 | 0.69 | 0.93 | 19 | empty |
| 3 | 213 | 0.67 | 0.85 | 33 | empty |
| 4 | 688 | 0.65 | 0.75 | 57 | empty |
| 5 | 204 | 0.65 | 0.84 | 32 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1867 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1764 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 641 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 426 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 422 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6PXH · Crystal Structure of MERS-CoV S1-NTD bound with G2 Fab · 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 V9TWK2
- Elsewhere: RCSB PDB 6PXH · PDBe 6PXH · UniProt V9TWK2
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