MolNFT v1 · #76190 · protein
Crystal structure of a putative ribose-5-phosphate isomerase from coccidioides immitis solved by combined iodide ion sad and mr
3QD5: “Crystal structure of a putative ribose-5-phosphate isomerase from coccidioides immitis solved by combined…”. X-ray diffraction, 1 ligand (IOD), 4 pockets (best druggability 0.56). MolNFT v1 #76190 on GenesisL1: 3D structure, binding…
- PDB
- 3QD5
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ribose-5-phosphate isomerase
- EC
- 5.3.1.6
- Ligands
- IOD
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative ribose-5-phosphate isomerase (EC 5.3.1.6) | protein | 160 | 43% helix, 20% strand | — |
| B | Putative ribose-5-phosphate isomerase (EC 5.3.1.6) | protein | 160 | 43% helix, 19% strand | — |
Ligands and binding sites
- IOD · Iodide ion · ion · 29 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.56 | 0.87 | 18 | empty |
| 2 | 92 | 0.49 | 0.82 | 15 | IOD |
| 3 | 94 | 0.37 | 0.76 | 19 | IOD |
| 4 | 55 | 0.25 | 0.73 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 1780 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3QD5 · Crystal structure of a putative ribose-5-phosphate isomerase from Coccidioides immitis… · 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
- Elsewhere: RCSB PDB 3QD5 · PDBe 3QD5
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