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R2-like ligand binding mn-fe oxidase from M. tuberculosis with an organized C-terminal helix
Analyse R2-like ligand binding mn-fe oxidase from M. tuberculosis with an organized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AC8
- Type
- protein
- Length
- 1,239 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R2-like ligand binding oxidase
- EC
- 1.17.4.1
- UniProt
- P96416
- Ligands
- MYR, FE, MN, CA
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | R2-like ligand binding oxidase (EC 1.17.4.1) | protein | 311 | 78% helix, 0% strand | P96416 |
| B, C | R2-like ligand binding oxidase (EC 1.17.4.1) | protein | 309 | 78% helix, 0% strand | P96416 |
| D | R2-like ligand binding oxidase (EC 1.17.4.1) | protein | 310 | 78% helix, 0% strand | P96416 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.83 | 0.98 | 30 | MYR |
| 2 | 168 | 0.82 | 0.97 | 28 | MYR |
| 3 | 166 | 0.82 | 0.97 | 28 | MYR |
| 4 | 164 | 0.81 | 0.97 | 28 | MYR |
| 5 | 273 | 0.71 | 0.85 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2590 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 2495 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 749 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4AC8 · R2-like ligand binding Mn-Fe oxidase from M. tuberculosis with an organized C-terminal… · 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 P96416
- Elsewhere: RCSB PDB 4AC8 · PDBe 4AC8 · UniProt P96416
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