Research workbench
Crystal structure of hyperthermophilic thermotoga maritima L-ribulose 3-epimerase with MN2+
Analyse Crystal structure of hyperthermophilic thermotoga maritima L-ribulose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H6H
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein TM_0416
- UniProt
- Q9WYP7
- Ligands
- MN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein TM_0416 | protein | 269 | 50% helix, 14% strand | Q9WYP7 |
| B | Uncharacterized protein TM_0416 | protein | 268 | 50% helix, 14% strand | Q9WYP7 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.74 | 0.79 | 77 | PGE, 1PE |
| 2 | 326 | 0.63 | 0.79 | 32 | empty |
| 3 | 296 | 0.63 | 0.80 | 38 | empty |
| 4 | 50 | 0.38 | 0.81 | 14 | empty |
| 5 | 50 | 0.24 | 0.72 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 544 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5H6H · Crystal Structure of Hyperthermophilic Thermotoga maritima L-Ribulose 3-Epimerase with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYP7 · AlphaFold monomer V2.0 prediction for 5-keto-L-gluconate epimerase (Q9WYP7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9WYP7
- Elsewhere: RCSB PDB 5H6H · PDBe 5H6H · UniProt Q9WYP7
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