MolNFT v1 · #113303 · protein
Structure of GH84 with ligand
5ABF · O-glcnacase BT_4395: “Structure of GH84 with ligand”. X-ray diffraction, 2 ligands (XRJ, CA), 20 pockets (best druggability 0.67). MolNFT v1 #113303 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ABF
- Type
- protein
- Length
- 1,314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase BT_4395
- EC
- 3.2.1.169
- UniProt
- Q89ZI2
- Ligands
- XRJ, CA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase BT_4395 (EC 3.2.1.169) | protein | 663 | 40% helix, 19% strand | Q89ZI2 |
| B | O-glcnacase BT_4395 (EC 3.2.1.169) | protein | 651 | 41% helix, 19% strand | Q89ZI2 |
Ligands and binding sites
- XRJ · 2-[(2S,3R,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.67 | 0.78 | 53 | empty |
| 2 | 415 | 0.64 | 0.78 | 56 | empty |
| 3 | 261 | 0.60 | 0.79 | 23 | empty |
| 4 | 104 | 0.58 | 0.85 | 20 | XRJ |
| 5 | 99 | 0.55 | 0.84 | 19 | XRJ |
Interfaces
1 interface between chains.
- A–B · 1110 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
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 Q89ZI2
- Elsewhere: RCSB PDB 5ABF · PDBe 5ABF · UniProt Q89ZI2
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