Research workbench
Crystal structure of an iclr homolog from microbacterium sp. strain HM58-2
Analyse Crystal structure of an iclr homolog from microbacterium sp. strain HM58-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H1A
- Type
- protein
- Length
- 962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iclr transcription factor homolog
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iclr transcription factor homolog | protein | 238 | 47% helix, 22% strand | — |
| B | Iclr transcription factor homolog | protein | 243 | 46% helix, 20% strand | — |
| C | Iclr transcription factor homolog | protein | 241 | 46% helix, 22% strand | — |
| D | Iclr transcription factor homolog | protein | 240 | 46% helix, 20% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.78 | 0.80 | 116 | empty |
| 2 | 126 | 0.70 | 0.91 | 28 | empty |
| 3 | 124 | 0.63 | 0.87 | 28 | empty |
| 4 | 356 | 0.63 | 0.78 | 46 | empty |
| 5 | 86 | 0.59 | 0.88 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2592 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2371 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 599 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 545 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 253 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5H1A · Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2 · 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
- Elsewhere: RCSB PDB 5H1A · PDBe 5H1A
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