Research workbench
Crystal structure of the padr-family transcriptional regulator RV3488 of mycobacterium tuberculosis H37RV in complex with cadmium ion
Analyse Crystal structure of the padr-family transcriptional regulator RV3488 of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZI8
- Type
- protein
- Length
- 207 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator
- UniProt
- I6X7F9
- Ligands
- CD
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator | protein | 104 | 63% helix, 16% strand | I6X7F9 |
| B | Transcriptional regulator | protein | 103 | 64% helix, 17% strand | I6X7F9 |
Ligands and binding sites
- CD · Cadmium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.33 | 0.77 | 14 | empty |
| 2 | 54 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1970 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5ZI8 · Crystal structure of the PadR-family transcriptional regulator Rv3488 of Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- I6X7F9 · AlphaFold monomer V2.0 prediction for transcriptional regulator RV3488 (I6X7F9) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 I6X7F9
- Elsewhere: RCSB PDB 5ZI8 · PDBe 5ZI8 · UniProt I6X7F9
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