MolNFT v1 · #60565 · protein
Crystal structure of a putative phosphoheptose isomerase (BH3325) from bacillus halodurans C-125 at 2.00 a resolution
3CVJ: “Crystal structure of a putative phosphoheptose isomerase (BH3325) from bacillus halodurans C-125 at 2.00 a…”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.85). MolNFT v1 #60565 on GenesisL1: 3D structure, binding…
- PDB
- 3CVJ
- Type
- protein
- Length
- 970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phosphoheptose isomerase
- UniProt
- Q9K7N6
- Ligands
- MG
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative phosphoheptose isomerase | protein | 243 | 48% helix, 12% strand | Q9K7N6 |
| C, D | Putative phosphoheptose isomerase | protein | 242 | 48% helix, 12% strand | Q9K7N6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.85 | 0.95 | 62 | ACT |
| 2 | 393 | 0.82 | 0.91 | 40 | EDO |
| 3 | 570 | 0.79 | 0.85 | 40 | EDO |
| 4 | 564 | 0.79 | 0.85 | 43 | empty |
| 5 | 731 | 0.79 | 0.83 | 61 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3295 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3085 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 781 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 779 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 109 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3CVJ · Crystal structure of a putative phosphoheptose isomerase (bh3325) from bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9K7N6 · AlphaFold monomer V2.0 prediction for UPF0309 protein BH3325 (Q9K7N6) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9K7N6
- Elsewhere: RCSB PDB 3CVJ · PDBe 3CVJ · UniProt Q9K7N6
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