MolNFT v1 · #126841 · protein
Crystal structure of a C-terminally truncated trimeric ectodomain of the chlamydomonas reinhardtii gamete fusion protein HAP2
5MF1 · Fusion protein HAP2/GCS1: “Crystal structure of a C-terminally truncated trimeric ectodomain of the chlamydomonas reinhardtii gamete…”. X-ray diffraction, 2 ligands (NAG, NGA), 20 pockets (best druggability 0.89). MolNFT v1 #126841…
- PDB
- 5MF1
- Type
- protein
- Length
- 1,329 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion protein HAP2/GCS1
- UniProt
- A4GRC6
- Ligands
- NAG, NGA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion protein HAP2/GCS1 | protein | 446 | 9% helix, 43% strand | A4GRC6 |
| B | Fusion protein HAP2/GCS1 | protein | 441 | 8% helix, 43% strand | A4GRC6 |
| C | Fusion protein HAP2/GCS1 | protein | 442 | 7% helix, 43% strand | A4GRC6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.89 | 0.91 | 138 | empty |
| 2 | 773 | 0.89 | 0.92 | 67 | empty |
| 3 | 397 | 0.85 | 0.93 | 43 | empty |
| 4 | 559 | 0.82 | 0.88 | 71 | empty |
| 5 | 403 | 0.81 | 0.90 | 44 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2837 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2830 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 2678 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 6 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 5MF1 · Crystal structure of a C-terminally truncated trimeric ectodomain of the Chlamydomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- A4GRC6 · AlphaFold monomer V2.0 prediction for hapless 2 (A4GRC6) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 A4GRC6
- Elsewhere: RCSB PDB 5MF1 · PDBe 5MF1 · UniProt A4GRC6
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