Research workbench
Crystal structure of D678A goxa soaked in glycine at pH 7.5
Analyse Crystal structure of D678A goxa soaked in 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
- 6UC1
- Type
- protein
- Length
- 3,105 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein goxa
- UniProt
- A0A161XU12
- Ligands
- GLY, MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uncharacterized protein goxa | protein | 776 | 31% helix, 20% strand | A0A161XU12 |
| A | Uncharacterized protein goxa | protein | 776 | 32% helix, 21% strand | A0A161XU12 |
| D | Uncharacterized protein goxa | protein | 776 | 31% helix, 20% strand | A0A161XU12 |
| C | Uncharacterized protein goxa | protein | 777 | 31% helix, 20% strand | A0A161XU12 |
Ligands and binding sites
- GLY · Glycine · ligand · 4 copies · chains B, A, D, C
- MG · Magnesium ion · metal · 4 copies · chains B, A, D, C
- SO4 · Sulfate ion · ion · 12 copies · chains B, A, D, C
- PGE · Triethylene glycol · additive · chains B, C
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 | 500 | 0.86 | 0.92 | 60 | GLY |
| 2 | 490 | 0.85 | 0.92 | 59 | GLY |
| 3 | 788 | 0.81 | 0.85 | 102 | empty |
| 4 | 1173 | 0.81 | 0.82 | 121 | empty |
| 5 | 144 | 0.76 | 0.94 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–A · 3066 Ų buried · 61 hydrogen bonds · protein-protein
- D–C · 3049 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 2230 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2226 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (cofactor, nonstandard).
Compared structures
- 6UC1 · Crystal structure of D678A GoxA soaked in glycine at pH 7.5 · 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 6UC1 · PDBe 6UC1 · UniProt A0A161XU12
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