Research workbench
Crystal structure of D678A goxa bound to glycine at pH 7.5
Analyse Crystal structure of D678A goxa bound to glycine at pH 7.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UBR
- Type
- protein
- Length
- 3,124 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A0A161XU12
- Ligands
- GLY, MG, SO4
- 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 | protein | 782 | 32% helix, 20% strand | A0A161XU12 |
| A | Uncharacterized protein | protein | 788 | 32% helix, 20% strand | A0A161XU12 |
| C | Uncharacterized protein | protein | 778 | 33% helix, 20% strand | A0A161XU12 |
| D | Uncharacterized protein | protein | 776 | 31% helix, 21% 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
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 464 | 0.86 | 0.93 | 53 | empty |
| 2 | 461 | 0.85 | 0.92 | 54 | empty |
| 3 | 982 | 0.81 | 0.83 | 103 | empty |
| 4 | 807 | 0.81 | 0.84 | 96 | empty |
| 5 | 142 | 0.76 | 0.94 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3051 Ų buried · 55 hydrogen bonds · protein-protein
- B–A · 3037 Ų buried · 60 hydrogen bonds · protein-protein
- B–D · 2178 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2158 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 370 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6UBR · Crystal structure of D678A GoxA bound to glycine at pH 7.5 · 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 6UBR · PDBe 6UBR · UniProt A0A161XU12
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.