Research workbench
X-ray structure of a rex-family REPRESSOR/NADH complex from thermus aquaticus
Analyse X-ray structure of a rex-family REPRESSOR/NADH complex from thermus aquaticus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XCB
- Type
- protein
- Length
- 1,397 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Redox-sensing transcriptional repressor rex
- UniProt
- Q9X2V5
- Ligands
- NAD, CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Redox-sensing transcriptional repressor rex | protein | 205 | 37% helix, 16% strand | Q9X2V5 |
| B | Redox-sensing transcriptional repressor rex | protein | 197 | 40% helix, 15% strand | Q9X2V5 |
| C | Redox-sensing transcriptional repressor rex | protein | 203 | 41% helix, 17% strand | Q9X2V5 |
| D | Redox-sensing transcriptional repressor rex | protein | 197 | 42% helix, 18% strand | Q9X2V5 |
| E | Redox-sensing transcriptional repressor rex | protein | 203 | 40% helix, 16% strand | Q9X2V5 |
| F | Redox-sensing transcriptional repressor rex | protein | 200 | 44% helix, 16% strand | Q9X2V5 |
| G | Redox-sensing transcriptional repressor rex | protein | 192 | 42% helix, 16% strand | Q9X2V5 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 7 copies · chains A, B, C, D, E, F, G
- CA · Calcium ion · metal · 5 copies · chains A, B, G, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.78 | 0.81 | 74 | empty |
| 2 | 543 | 0.77 | 0.84 | 57 | NAD |
| 3 | 938 | 0.74 | 0.78 | 79 | empty |
| 4 | 602 | 0.73 | 0.80 | 67 | CA |
| 5 | 170 | 0.65 | 0.85 | 35 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2683 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2599 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2587 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 522 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 501 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1XCB · X-ray Structure of a Rex-Family Repressor/NADH Complex from Thermus Aquaticus · the same entry in another collection · chain G against G, TM-score 1.00
- Q9X2V5 · AlphaFold monomer V2.0 prediction for redox-sensing transcriptional repressor rex (Q9X2V5) · a predicted model of the same protein · chain E against A, TM-score 0.94
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 Q9X2V5
- Elsewhere: RCSB PDB 1XCB · PDBe 1XCB · UniProt Q9X2V5
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