MolNFT v1 · #57496 · protein
Crystal structure of ribose-1,5-bisphosphate isomerase from thermococcus kodakaraensis KOD1 in complex with ribulose-1,5- bisphosphate
3A9C · Translation initiation factor eif-2B, delta subunit: “Crystal structure of ribose-1,5-bisphosphate isomerase from thermococcus kodakaraensis KOD1 in complex with…”. X-ray diffraction, 2 ligands (RUB, MG), 16 pockets (best…
- PDB
- 3A9C
- Type
- protein
- Length
- 1,931 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor eif-2B, delta subunit
- EC
- 5.3.1.-
- UniProt
- Q5JFM9
- Ligands
- RUB, MG
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 320 | 51% helix, 14% strand | Q5JFM9 |
| B | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 325 | 49% helix, 14% strand | Q5JFM9 |
| C, E | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 321 | 48% helix, 15% strand | Q5JFM9 |
| D, F | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 322 | 50% helix, 13% strand | Q5JFM9 |
Ligands and binding sites
- RUB · Ribulose-1,5-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, C, E, B, D, F
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.84 | 0.90 | 85 | PEG |
| 2 | 266 | 0.77 | 0.90 | 44 | PEG |
| 3 | 987 | 0.76 | 0.79 | 112 | MG |
| 4 | 362 | 0.75 | 0.86 | 41 | PEG |
| 5 | 293 | 0.73 | 0.87 | 40 | PEG |
Interfaces
12 interfaces between chains.
- C–D · 2232 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2167 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2162 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 879 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 847 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (oxidation).
Compared structures
- 3A9C · Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis… · the same entry in another collection · chain F against F, TM-score 1.00
- Q5JFM9 · AlphaFold monomer V2.0 prediction for ribose 1,5-bisphosphate isomerase (Q5JFM9) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 Q5JFM9
- Elsewhere: RCSB PDB 3A9C · PDBe 3A9C · UniProt Q5JFM9
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