Research workbench
Crystal structure of D678A goxa bound to glycine at pH 5.5
Analyse Crystal structure of D678A goxa bound to glycine at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UBZ
- Type
- protein
- Length
- 3,139 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein goxa
- UniProt
- A0A161XU12
- Ligands
- GLY, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uncharacterized protein goxa | protein | 783 | 31% helix, 20% strand | A0A161XU12 |
| A | Uncharacterized protein goxa | protein | 791 | 32% helix, 20% strand | A0A161XU12 |
| C | Uncharacterized protein goxa | protein | 785 | 32% helix, 20% strand | A0A161XU12 |
| D | Uncharacterized protein goxa | protein | 780 | 32% helix, 20% strand | A0A161XU12 |
Ligands and binding sites
- GLY · Glycine · ligand · 4 copies · chains B, A, C, D
- MG · Magnesium ion · metal · 4 copies · chains B, A, C, D
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 | 479 | 0.86 | 0.92 | 58 | GLY |
| 2 | 471 | 0.85 | 0.92 | 57 | GLY |
| 3 | 962 | 0.83 | 0.85 | 120 | empty |
| 4 | 160 | 0.78 | 0.95 | 34 | empty |
| 5 | 704 | 0.78 | 0.82 | 75 | empty |
Interfaces
6 interfaces between chains.
- B–A · 3082 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 3070 Ų buried · 62 hydrogen bonds · protein-protein
- B–D · 2318 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2251 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 343 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6UBZ · Crystal structure of D678A GoxA bound to glycine at pH 5.5 · the same entry in another collection · chain B against B, 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 6UBZ · PDBe 6UBZ · UniProt A0A161XU12
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.