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Crystal structure of an uronate isomerase (BH0493) from bacillus halodurans C-125 at 2.00 a resolution
Analyse Crystal structure of an uronate isomerase (BH0493) from bacillus halodurans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PNK
- Type
- protein
- Length
- 5,041 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BH0493 protein
- UniProt
- Q9KFI6
- Ligands
- UNL, MSE, NA, CL, PO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 10 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | BH0493 protein | protein | 424 | 57% helix, 9% strand | Q9KFI6 |
| B, G | BH0493 protein | protein | 423 | 58% helix, 10% strand | Q9KFI6 |
| C | BH0493 protein | protein | 420 | 56% helix, 9% strand | Q9KFI6 |
| D | BH0493 protein | protein | 414 | 58% helix, 9% strand | Q9KFI6 |
| E | BH0493 protein | protein | 418 | 57% helix, 9% strand | Q9KFI6 |
| F | BH0493 protein | protein | 413 | 58% helix, 9% strand | Q9KFI6 |
| H | BH0493 protein | protein | 421 | 57% helix, 9% strand | Q9KFI6 |
| I | BH0493 protein | protein | 420 | 58% helix, 9% strand | Q9KFI6 |
| J | BH0493 protein | protein | 419 | 58% helix, 9% strand | Q9KFI6 |
| L | BH0493 protein | protein | 422 | 58% helix, 9% strand | Q9KFI6 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 3 copies · chains B, G, A, H, J
- MSE · Selenomethionine · ligand · chains J
- NA · Sodium ion · metal · 3 copies · chains A, B, C, G, H, I, J, K, L
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PO4 · Phosphate ion · ion · 4 copies · chains C, D, F, K
- GOL · Glycerol · additive · 24 copies · chains A, B, D, F, E, G, H, I, J, K, L
- FMT · Formic acid · additive · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains C, G, K, L
- ACT · Acetate ion · additive · 3 copies · chains F, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.75 | 0.78 | 94 | GOL |
| 2 | 572 | 0.73 | 0.81 | 59 | empty |
| 3 | 404 | 0.68 | 0.81 | 44 | empty |
| 4 | 345 | 0.68 | 0.82 | 34 | empty |
| 5 | 421 | 0.67 | 0.80 | 43 | NA |
Interfaces
28 interfaces between chains.
- J–L · 2082 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2072 Ų buried · 37 hydrogen bonds · protein-protein
- G–I · 2071 Ų buried · 37 hydrogen bonds · protein-protein
- H–I · 2064 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2061 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 199 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 2PNK · Crystal structure of an uronate isomerase (BH0493) from bacillus halodurans C-125 at 2.00… · 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 Q9KFI6
- Elsewhere: RCSB PDB 2PNK · PDBe 2PNK · UniProt Q9KFI6
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