MolNFT v1 · #53744 · protein
Crystal structure of gmha from burkholderia pseudomallei
2X3Y · Phosphoheptose isomerase: “Crystal structure of gmha from burkholderia pseudomallei”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.73). MolNFT v1 #53744 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2X3Y
- Type
- protein
- Length
- 1,548 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoheptose isomerase
- EC
- 5.3.1.-
- UniProt
- Q93UJ2
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoheptose isomerase (EC 5.3.1.-) | protein | 202 | 60% helix, 11% strand | Q93UJ2 |
| B, D, E | Phosphoheptose isomerase (EC 5.3.1.-) | protein | 193 | 60% helix, 11% strand | Q93UJ2 |
| C, F, G | Phosphoheptose isomerase (EC 5.3.1.-) | protein | 192 | 58% helix, 11% strand | Q93UJ2 |
| H | Phosphoheptose isomerase (EC 5.3.1.-) | protein | 191 | 61% helix, 12% strand | Q93UJ2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.73 | 0.98 | 21 | empty |
| 2 | 63 | 0.73 | 0.98 | 22 | empty |
| 3 | 65 | 0.72 | 0.97 | 21 | empty |
| 4 | 60 | 0.70 | 0.96 | 23 | empty |
| 5 | 539 | 0.68 | 0.78 | 62 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1934 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1836 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1822 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1778 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1229 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
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 2X3Y · PDBe 2X3Y · UniProt Q93UJ2
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