Research workbench
Crystal structure of gmha from burkholderia pseudomallei in complex with product
Analyse Crystal structure of gmha from burkholderia pseudomallei in complex with product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XBL
- Type
- protein
- Length
- 775 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoheptose isomerase
- EC
- 5.3.1.-
- UniProt
- Q93UJ2
- Ligands
- M7P, ZN
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoheptose isomerase (EC 5.3.1.-) | protein | 194 | 59% helix, 11% strand | Q93UJ2 |
| B, C | Phosphoheptose isomerase (EC 5.3.1.-) | protein | 193 | 60% helix, 11% strand | Q93UJ2 |
| D | Phosphoheptose isomerase (EC 5.3.1.-) | protein | 195 | 59% helix, 11% strand | Q93UJ2 |
Ligands and binding sites
- M7P · 7-O-phosphono-D-glycero-alpha-D-manno-heptopyranose · ligand · 4 copies · chains A, B, D, C
- ZN · Zinc ion · metal · 4 copies · chains A, D, B, C
- PG4 · Tetraethylene glycol · additive · chains A
- PGE · Triethylene glycol · additive · chains C
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 53 | 0.72 | 0.99 | 20 | empty |
| 2 | 52 | 0.69 | 0.97 | 20 | empty |
| 3 | 183 | 0.59 | 0.82 | 36 | M7P |
| 4 | 162 | 0.58 | 0.83 | 25 | M7P |
| 5 | 150 | 0.57 | 0.83 | 25 | M7P |
Interfaces
6 interfaces between chains.
- A–D · 1815 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1802 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1212 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1210 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 703 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2XBL · Crystal structure of GmhA from Burkholderia pseudomallei in complex with product · the same entry in another collection · chain A against A, TM-score 1.00
- Q93UJ2 · AlphaFold monomer V2.0 prediction for phosphoheptose isomerase (Q93UJ2) · a predicted model of the same protein · chain B 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 Q93UJ2
- Elsewhere: RCSB PDB 2XBL · PDBe 2XBL · UniProt Q93UJ2
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