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Crystal structure of an indigoidine synthase a (idga)-like protein (TM1464) from thermotoga maritima MSB8 at 1.90 a resolution
Analyse Crystal structure of an indigoidine synthase a (idga)-like protein (TM1464)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VKM
- Type
- protein
- Length
- 1,752 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Conserved hypothetical protein TM1464
- UniProt
- Q9X1H5
- Ligands
- UNL, MN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Conserved hypothetical protein TM1464 | protein | 292 | 46% helix, 18% strand | Q9X1H5 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 6 copies · chains A, C, B, D, E, F
- MN · Manganese (II) ion · metal · 16 copies · chains A, C, E, B, F, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, E, B, C, F, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.84 | 0.85 | 72 | empty |
| 2 | 1141 | 0.82 | 0.83 | 80 | EDO |
| 3 | 146 | 0.79 | 0.96 | 39 | MN, UNL |
| 4 | 198 | 0.79 | 0.93 | 42 | MN, UNL, EDO |
| 5 | 148 | 0.79 | 0.96 | 37 | MN, UNL |
Interfaces
12 interfaces between chains.
- E–F · 1309 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1282 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1277 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1276 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1249 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 1VKM · Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9X1H5 · AlphaFold monomer V2.0 prediction for pseudouridine-5'-phosphate glycosidase (Q9X1H5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9X1H5
- Elsewhere: RCSB PDB 1VKM · PDBe 1VKM · UniProt Q9X1H5
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