MolNFT v1 · #165957 · protein
Crystal structure of D678E goxa bound to glycine
6UBN · Quinoprotein glycine oxidase: “Crystal structure of D678E goxa bound to glycine”. X-ray diffraction, 2 ligands (MG, NA), 20 pockets (best druggability 0.87). MolNFT v1 #165957 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6UBN
- Type
- protein
- Length
- 3,133 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quinoprotein glycine oxidase
- UniProt
- A0A161XU12
- Ligands
- MG, NA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quinoprotein glycine oxidase | protein | 784 | 32% helix, 20% strand | A0A161XU12 |
| B | Quinoprotein glycine oxidase | protein | 791 | 32% helix, 21% strand | A0A161XU12 |
| C | Quinoprotein glycine oxidase | protein | 771 | 30% helix, 21% strand | A0A161XU12 |
| D | Quinoprotein glycine oxidase | protein | 787 | 31% helix, 21% strand | A0A161XU12 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.87 | 0.92 | 80 | empty |
| 2 | 480 | 0.85 | 0.92 | 55 | empty |
| 3 | 724 | 0.79 | 0.83 | 72 | empty |
| 4 | 678 | 0.78 | 0.83 | 67 | empty |
| 5 | 160 | 0.77 | 0.94 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3078 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 3039 Ų buried · 66 hydrogen bonds · protein-protein
- B–C · 2510 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 2509 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 263 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6UBN · Crystal structure of D678E GoxA bound to glycine · 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 A0A161XU12
- Elsewhere: RCSB PDB 6UBN · PDBe 6UBN · UniProt A0A161XU12
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