MolNFT v1 · #60518 · protein
Crystal structure of ribulose-5-phosphate 3-epimerase (YP_718263.1) from haemophilus somnus 129PT at 1.91 a resolution
3CU2: “Crystal structure of ribulose-5-phosphate 3-epimerase (YP_718263.1) from haemophilus somnus 129PT at 1.91 a…”. X-ray diffraction, 2 ligands (CA, NI), 4 pockets (best druggability 0.62). MolNFT v1 #60518 on GenesisL1: 3D structure…
- PDB
- 3CU2
- Type
- protein
- Length
- 471 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-5-phosphate 3-epimerase
- EC
- 5.1.3.1
- UniProt
- Q0I165
- Ligands
- CA, NI
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) | protein | 235 | 40% helix, 24% strand | Q0I165 |
| B | Ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) | protein | 236 | 41% helix, 22% strand | Q0I165 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.62 | 0.79 | 44 | empty |
| 2 | 81 | 0.58 | 0.87 | 14 | MRD |
| 3 | 276 | 0.58 | 0.78 | 31 | empty |
| 4 | 72 | 0.54 | 0.86 | 13 | MRD |
Interfaces
1 interface between chains.
- A–B · 1093 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3CU2 · Crystal structure of ribulose-5-phosphate 3-epimerase (YP_718263.1) from Haemophilus… · 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 Q0I165
- Elsewhere: RCSB PDB 3CU2 · PDBe 3CU2 · UniProt Q0I165
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