MolNFT v1 · #57223 · protein
Crystal structure of ribose-1,5-bisphosphate isomerase from thermococcus kodakaraensis KOD1
3A11 · Translation initiation factor eif-2B, delta subunit: “Crystal structure of ribose-1,5-bisphosphate isomerase from thermococcus kodakaraensis KOD1”. X-ray diffraction, 1 ligand (MG), 18 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 3A11
- Type
- protein
- Length
- 1,915 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
- MG
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 5 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 | 49% helix, 14% strand | Q5JFM9 |
| B | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 322 | 49% helix, 15% strand | Q5JFM9 |
| C, E | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 317 | 49% helix, 14% strand | Q5JFM9 |
| D | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 320 | 48% helix, 14% strand | Q5JFM9 |
| F | Translation initiation factor eif-2B, delta subunit (EC 5.3.1.-) | protein | 319 | 50% helix, 14% strand | Q5JFM9 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, D, F, A, C, E
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.85 | 0.87 | 101 | PEG |
| 2 | 622 | 0.83 | 0.88 | 77 | PEG |
| 3 | 1034 | 0.74 | 0.77 | 101 | empty |
| 4 | 830 | 0.71 | 0.77 | 79 | empty |
| 5 | 232 | 0.70 | 0.86 | 33 | MG |
Interfaces
12 interfaces between chains.
- C–D · 2151 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2139 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2097 Ų buried · 32 hydrogen bonds · protein-protein
- C–E · 813 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 791 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3A11 · 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 C against A, TM-score 0.82
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 3A11 · PDBe 3A11 · UniProt Q5JFM9
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