MolNFT v1 · #157755 · protein
Xylose isomerase 2F1 variant from streptomyces sp. F-1
6N99: “Xylose isomerase 2F1 variant from streptomyces sp. F-1”. X-ray diffraction, 2 ligands (MG, SO4), 17 pockets (best druggability 0.85). MolNFT v1 #157755 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6N99
- Type
- protein
- Length
- 1,536 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- A0A1K2FKX8
- Ligands
- MG, SO4
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xylose isomerase (EC 5.3.1.5) | protein | 384 | 49% helix, 9% strand | A0A1K2FKX8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.85 | 0.90 | 106 | empty |
| 2 | 617 | 0.85 | 0.90 | 98 | empty |
| 3 | 1077 | 0.84 | 0.84 | 108 | MG |
| 4 | 524 | 0.76 | 0.83 | 60 | empty |
| 5 | 66 | 0.75 | 0.99 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–D · 4836 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 4756 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 1617 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1563 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1527 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 6N99 · Xylose isomerase 2F1 variant from Streptomyces sp. F-1 · 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 A0A1K2FKX8
- Elsewhere: RCSB PDB 6N99 · PDBe 6N99 · UniProt A0A1K2FKX8
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