MolNFT v1 · #136924 · protein
Prolyl 4-hydroxylase interacts with and modifies elongation factor tu
5V7Y · 2OG-FE(II) oxygenase: “Prolyl 4-hydroxylase interacts with and modifies elongation factor tu”. X-ray diffraction, 2 ligands (AKG, CO), 11 pockets (best druggability 0.74). MolNFT v1 #136924 on GenesisL1: 3D structure, binding sites…
- PDB
- 5V7Y
- Type
- protein
- Length
- 816 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2OG-FE(II) oxygenase
- UniProt
- A0A0F7R8C5
- Ligands
- AKG, CO
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2OG-FE(II) oxygenase | protein | 207 | 17% helix, 31% strand | A0A0F7R8C5 |
| B | 2OG-FE(II) oxygenase | protein | 206 | 23% helix, 31% strand | A0A0F7R8C5 |
| D | 2OG-FE(II) oxygenase | protein | 201 | 25% helix, 33% strand | A0A0F7R8C5 |
| C | 2OG-FE(II) oxygenase | protein | 202 | 22% helix, 33% strand | A0A0F7R8C5 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, D, C
- IMD · Imidazole · additive · 5 copies · chains A, D, C
- TFA · trifluoroacetic acid · additive · 3 copies · chains A, D, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.74 | 0.98 | 20 | empty |
| 2 | 61 | 0.70 | 0.96 | 19 | IMD, TFA |
| 3 | 631 | 0.68 | 0.77 | 51 | IMD |
| 4 | 116 | 0.58 | 0.85 | 29 | IMD, TFA |
| 5 | 254 | 0.55 | 0.77 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1178 Ų buried · 24 hydrogen bonds · protein-protein
- D–C · 1154 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 532 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5V7Y · Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu · 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 A0A0F7R8C5
- Elsewhere: RCSB PDB 5V7Y · PDBe 5V7Y · UniProt A0A0F7R8C5
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