Research workbench
Crystal structure of a putative iclr transcriptional regulator (TM1040_3717) from silicibacter sp. TM1040 at 2.46 a resolution
Analyse Crystal structure of a putative iclr transcriptional regulator (TM1040_3717)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R4K
- Type
- protein
- Length
- 1,017 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, iclr family
- UniProt
- Q1GKY2
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transcriptional regulator, iclr family | protein | 255 | 44% helix, 22% strand | Q1GKY2 |
| B | Transcriptional regulator, iclr family | protein | 254 | 45% helix, 21% strand | Q1GKY2 |
| D | Transcriptional regulator, iclr family | protein | 253 | 44% helix, 22% strand | Q1GKY2 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.74 | 0.98 | 21 | EDO |
| 2 | 84 | 0.68 | 0.93 | 25 | empty |
| 3 | 86 | 0.65 | 0.91 | 27 | empty |
| 4 | 116 | 0.62 | 0.87 | 29 | EDO |
| 5 | 303 | 0.56 | 0.76 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1935 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1930 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 525 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 486 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 3R4K · Crystal structure of a putative ICLR transcriptional regulator (TM1040_3717) from… · the same entry in another collection · chain B against B, 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 Q1GKY2
- Elsewhere: RCSB PDB 3R4K · PDBe 3R4K · UniProt Q1GKY2
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