MolNFT v1 · #126455 · protein
Macrodomain of mycobacterium tuberculosis darg
5M3I · RNase III inhibitor: “Macrodomain of mycobacterium tuberculosis darg”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.73). MolNFT v1 #126455 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M3I
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNase III inhibitor
- UniProt
- A0A045JW26
- Ligands
- CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNase III inhibitor | protein | 152 | 36% helix, 18% strand | A0A045JW26 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.73 | 0.76 | 98 | CL |
| 2 | 322 | 0.66 | 0.81 | 45 | empty |
| 3 | 213 | 0.59 | 0.81 | 38 | empty |
| 4 | 180 | 0.57 | 0.81 | 29 | empty |
| 5 | 74 | 0.30 | 0.73 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–C · 647 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 208 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 96 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 51 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 48 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5M3I · Macrodomain of Mycobacterium tuberculosis DarG · 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 A0A045JW26
- Elsewhere: RCSB PDB 5M3I · PDBe 5M3I · UniProt A0A045JW26
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