Research workbench
Crystal structure of a pseudomonas putida prolyl-4-hydroxylase (P4H) in complex with elongation factor tu (ef-tu)
Analyse Crystal structure of a pseudomonas putida prolyl-4-hydroxylase (P4H) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IW3
- Type
- protein
- Length
- 1,160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein; Elongation factor tu-a
- UniProt
- Q88CM1, Q88QP8
- Ligands
- OGA, GDP, MN, MG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Putative uncharacterized protein | protein | 201 | 29% helix, 34% strand | Q88CM1 |
| B | Elongation factor tu-a | protein | 380 | 21% helix, 38% strand | Q88QP8 |
| K | Elongation factor tu-a | protein | 378 | 21% helix, 38% strand | Q88QP8 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B, K, J
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, K
- MN · Manganese (II) ion · metal · 2 copies · chains A, B, K, J
- MG · Magnesium ion · metal · 2 copies · chains B, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.73 | 1.00 | 18 | MN, OGA |
| 2 | 1067 | 0.73 | 0.76 | 93 | empty |
| 3 | 52 | 0.72 | 0.99 | 18 | MN, OGA |
| 4 | 949 | 0.70 | 0.75 | 64 | empty |
| 5 | 164 | 0.48 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- K–J · 1811 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1778 Ų buried · 29 hydrogen bonds · protein-protein
- A–J · 585 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4IW3 · Crystal structure of a Pseudomonas putida prolyl-4-hydroxylase (P4H) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q88QP8 · AlphaFold monomer V2.0 prediction for elongation factor tu-a (Q88QP8) · a predicted model of the same protein · chain K against A, TM-score 0.57
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 Q88CM1
- Every structure of UniProt Q88QP8
- Elsewhere: RCSB PDB 4IW3 · PDBe 4IW3 · UniProt Q88CM1 · UniProt Q88QP8
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