MolNFT v1 · #128127 · protein
Crystal structure of xylose isomerase from piromyces E2 in complex with two FE2+ ions
5NHB: “Crystal structure of xylose isomerase from piromyces E2 in complex with two FE2+ ions”. X-ray diffraction, 2 ligands (FE2, SO4), 20 pockets (best druggability 0.90). MolNFT v1 #128127 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NHB
- Type
- protein
- Length
- 1,742 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- Q9P8C9
- Ligands
- FE2, SO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xylose isomerase (EC 5.3.1.5) | protein | 436 | 48% helix, 12% strand | Q9P8C9 |
| C, D | Xylose isomerase (EC 5.3.1.5) | protein | 435 | 48% helix, 12% strand | Q9P8C9 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.90 | 0.94 | 128 | empty |
| 2 | 1112 | 0.90 | 0.92 | 167 | FE2 |
| 3 | 355 | 0.83 | 0.93 | 72 | empty |
| 4 | 348 | 0.75 | 0.86 | 52 | empty |
| 5 | 331 | 0.74 | 0.86 | 52 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4342 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 4342 Ų buried · 55 hydrogen bonds · protein-protein
- A–D · 1965 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1958 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1520 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5NHB · Crystal structure of xylose isomerase from Piromyces E2 in complex with two Fe2+ ions · 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 Q9P8C9
- Elsewhere: RCSB PDB 5NHB · PDBe 5NHB · UniProt Q9P8C9
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