Research workbench
Structure of glycine-bound goxa from pseudoalteromonas luteoviolacea
Analyse Structure of glycine-bound goxa from pseudoalteromonas luteoviolacea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EER
- Type
- protein
- Length
- 3,115 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Goxa
- UniProt
- A0A161XU12
- Ligands
- MG, NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Goxa | protein | 768 | 31% helix, 21% strand | A0A161XU12 |
| B | Goxa | protein | 786 | 32% helix, 20% strand | A0A161XU12 |
| C | Goxa | protein | 777 | 32% helix, 20% strand | A0A161XU12 |
| D | Goxa | protein | 784 | 33% helix, 21% strand | A0A161XU12 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · chains C, D
- EDO · 1,2-ethanediol · additive · chains 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 | 458 | 0.85 | 0.92 | 56 | empty |
| 2 | 445 | 0.85 | 0.92 | 55 | empty |
| 3 | 150 | 0.78 | 0.95 | 32 | empty |
| 4 | 698 | 0.78 | 0.83 | 66 | PEG |
| 5 | 530 | 0.78 | 0.85 | 61 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3130 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 3067 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 2476 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2468 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 306 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 6EER · Structure of glycine-bound GoxA from Pseudoalteromonas luteoviolacea · 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 6EER · PDBe 6EER · UniProt A0A161XU12
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