Research workbench
Crystal structure of iclr family transcriptional regulator from brucella abortus
Analyse Crystal structure of iclr family transcriptional regulator from brucella abortus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WHM
- Type
- protein
- Length
- 1,047 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iclr family transcriptional regulator
- UniProt
- A0A1S1ZDZ5
- Ligands
- CA
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iclr family transcriptional regulator | protein | 263 | 46% helix, 19% strand | A0A1S1ZDZ5 |
| B | Iclr family transcriptional regulator | protein | 260 | 47% helix, 19% strand | A0A1S1ZDZ5 |
| C | Iclr family transcriptional regulator | protein | 264 | 47% helix, 20% strand | A0A1S1ZDZ5 |
| D | Iclr family transcriptional regulator | protein | 260 | 48% helix, 19% strand | A0A1S1ZDZ5 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- ACY · Acetic acid · additive · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.80 | 0.83 | 91 | ACY |
| 2 | 840 | 0.72 | 0.77 | 86 | ACY |
| 3 | 465 | 0.70 | 0.81 | 41 | empty |
| 4 | 86 | 0.63 | 0.90 | 17 | empty |
| 5 | 279 | 0.62 | 0.80 | 29 | EDO |
Interfaces
5 interfaces between chains.
- B–D · 3281 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 3277 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 528 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 235 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 87 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 modified (engineered).
Compared structures
- 5WHM · Crystal Structure of IclR Family Transcriptional Regulator from Brucella abortus · 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 A0A1S1ZDZ5
- Elsewhere: RCSB PDB 5WHM · PDBe 5WHM · UniProt A0A1S1ZDZ5
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