Research workbench
Structure of RV0554 from mycobacterium tuberculosis complexed with malonic acid
Analyse Structure of RV0554 from mycobacterium tuberculosis complexed with malonic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HYS
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein RV0554, putative bromoperoxidase
- EC
- 1.11.1.-
- UniProt
- O06420
- Ligands
- NA
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein RV0554, putative bromoperoxidase (EC 1.11.1.-) | protein | 275 | 45% helix, 19% strand | O06420 |
| B | Protein RV0554, putative bromoperoxidase (EC 1.11.1.-) | protein | 261 | 48% helix, 15% strand | O06420 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- MLA · Malonic acid · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.82 | 0.86 | 62 | MLA, TRS, EDO |
| 2 | 648 | 0.82 | 0.86 | 54 | MLA, EDO |
| 3 | 64 | 0.66 | 0.94 | 22 | empty |
| 4 | 117 | 0.60 | 0.85 | 24 | EDO |
Interfaces
1 interface between chains.
- A–B · 1658 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3HYS · Structure of Rv0554 from Mycobacterium tuberculosis complexed with Malonic Acid · 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 O06420
- Elsewhere: RCSB PDB 3HYS · PDBe 3HYS · UniProt O06420
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