MolNFT v1 · #177897 · protein
An AA9 lpmo of ceriporiopsis subvermispora
7EXK · Glycoside hydrolase family 61 protein: “An AA9 lpmo of ceriporiopsis subvermispora”. X-ray diffraction, 4 ligands (NAG, XYS, CU), 7 pockets (best druggability 0.73). MolNFT v1 #177897 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7EXK
- Type
- protein
- Length
- 1,302 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 61 protein
- UniProt
- M2RAI8
- Ligands
- NAG, XYS, CU, CA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glycoside hydrolase family 61 protein | protein | 217 | 4% helix, 33% strand | M2RAI8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
- XYS · alpha-D-xylopyranose · sugar · chains B
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 2 copies · chains C, D, F
- EDO · 1,2-ethanediol · additive · 66 copies · chains A, D, B, F, C, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.73 | 0.82 | 63 | EDO |
| 2 | 240 | 0.60 | 0.80 | 47 | empty |
| 3 | 285 | 0.55 | 0.76 | 28 | TRS |
| 4 | 223 | 0.53 | 0.77 | 43 | EDO |
| 5 | 137 | 0.48 | 0.79 | 30 | empty |
Interfaces
9 interfaces between chains.
- B–F · 475 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 344 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 190 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 169 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 168 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 7EXK · An AA9 LPMO of Ceriporiopsis subvermispora · 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 M2RAI8
- Elsewhere: RCSB PDB 7EXK · PDBe 7EXK · UniProt M2RAI8
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