MolNFT v1 · #180862 · protein
Crystal structure of a ribose-5-phosphate isomerase from stenotrophomonas maltophilia K279A
7LDA · Ribose-5-phosphate isomerase a: “Crystal structure of a ribose-5-phosphate isomerase from stenotrophomonas maltophilia K279A”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.38). MolNFT v1 #180862 on GenesisL1: 3D…
- PDB
- 7LDA
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-5-phosphate isomerase a
- EC
- 5.3.1.6
- UniProt
- B2FT30
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 215 | 36% helix, 27% strand | B2FT30 |
| B | Ribose-5-phosphate isomerase a (EC 5.3.1.6) | protein | 216 | 35% helix, 28% strand | B2FT30 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.38 | 0.81 | 19 | EDO, SO4 |
| 2 | 59 | 0.37 | 0.80 | 18 | EDO, SO4 |
Interfaces
1 interface between chains.
- A–B · 1369 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7LDA · Crystal structure of a ribose-5-phosphate isomerase from Stenotrophomonas maltophilia… · the same entry in another collection · chain A against A, TM-score 1.00
- B2FT30 · AlphaFold monomer V2.0 prediction for ribose-5-phosphate isomerase a (B2FT30) · a predicted model of the same protein · 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 B2FT30
- Elsewhere: RCSB PDB 7LDA · PDBe 7LDA · UniProt B2FT30
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