MolNFT v1 · #121592 · protein
Structure of phosphoheptose isomerase gmha from neisseria gonorrhoeae
5I01: “Structure of phosphoheptose isomerase gmha from neisseria gonorrhoeae”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.72). MolNFT v1 #121592 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I01
- Type
- protein
- Length
- 733 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoheptose isomerase
- EC
- 5.3.1.28
- UniProt
- Q5F5E3
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoheptose isomerase (EC 5.3.1.28) | protein | 184 | 60% helix, 14% strand | Q5F5E3 |
| C | Phosphoheptose isomerase (EC 5.3.1.28) | protein | 181 | 60% helix, 14% strand | Q5F5E3 |
| D | Phosphoheptose isomerase (EC 5.3.1.28) | protein | 184 | 59% helix, 14% strand | Q5F5E3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D, B, C
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 | 62 | 0.72 | 0.98 | 24 | empty |
| 2 | 60 | 0.72 | 0.98 | 24 | empty |
| 3 | 252 | 0.54 | 0.77 | 33 | empty |
| 4 | 249 | 0.53 | 0.77 | 35 | empty |
| 5 | 240 | 0.52 | 0.76 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1866 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1860 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1101 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1089 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 694 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5I01 · Structure of phosphoheptose isomerase GmhA from Neisseria gonorrhoeae · the same entry in another collection · chain A against A, TM-score 1.00
- Q5F5E3 · AlphaFold monomer V2.0 prediction for phosphoheptose isomerase (Q5F5E3) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q5F5E3
- Elsewhere: RCSB PDB 5I01 · PDBe 5I01 · UniProt Q5F5E3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.