MolNFT v1 · #16825 · protein
Glucose isomerase from streptomyces rubiginosus in P21212 crystal form
1OAD · Xylose isomerase: “Glucose isomerase from streptomyces rubiginosus in P21212 crystal form”. X-ray diffraction, 3 ligands (MQD, MN, MG), 10 pockets (best druggability 0.75). MolNFT v1 #16825 on GenesisL1: 3D structure, binding sites…
- PDB
- 1OAD
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- MQD, MN, MG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase (EC 5.3.1.5) | protein | 387 | 50% helix, 11% strand | P24300 |
| B | Xylose isomerase (EC 5.3.1.5) | protein | 386 | 50% helix, 11% strand | P24300 |
Ligands and binding sites
- MQD · 2-methylpentane-1,2,4-triol · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.75 | 0.96 | 21 | empty |
| 2 | 111 | 0.75 | 0.95 | 24 | empty |
| 3 | 58 | 0.73 | 0.99 | 25 | empty |
| 4 | 406 | 0.72 | 0.83 | 43 | MRD, MQD |
| 5 | 407 | 0.71 | 0.83 | 46 | MQD, MRD |
Interfaces
1 interface between chains.
- A–B · 1662 Ų buried · 26 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 P24300
- Elsewhere: RCSB PDB 1OAD · PDBe 1OAD · UniProt P24300
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