MolNFT v1 · #51331 · protein
Crystal structure of the semet-labeled prolyl-4 hydroxylase (P4H) type I from green algae chlamydomonas reinhardtii.
2V4A: “Crystal structure of the semet-labeled prolyl-4 hydroxylase (P4H) type I from green algae chlamydomonas…”. X-ray diffraction, 2 ligands (CL, SO4), 7 pockets (best druggability 0.72). MolNFT v1 #51331 on GenesisL1: 3D structure…
- PDB
- 2V4A
- Type
- protein
- Length
- 737 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl-4 hydroxylase
- Ligands
- CL, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl-4 hydroxylase | protein | 182 | 20% helix, 34% strand | — |
| B | Prolyl-4 hydroxylase | protein | 174 | 21% helix, 34% strand | — |
| C | Prolyl-4 hydroxylase | protein | 187 | 21% helix, 33% strand | — |
| D | Prolyl-4 hydroxylase | protein | 194 | 21% helix, 31% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B, C
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 | 469 | 0.72 | 0.81 | 46 | GOL |
| 2 | 65 | 0.64 | 0.92 | 16 | empty |
| 3 | 287 | 0.61 | 0.79 | 35 | empty |
| 4 | 62 | 0.52 | 0.87 | 25 | empty |
| 5 | 117 | 0.50 | 0.80 | 15 | DMS |
Interfaces
3 interfaces between chains.
- B–C · 909 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 418 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 405 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 3 disulfide (engineered, disulfide).
Compared structures
- 2V4A · Crystal structure of the SeMet-labeled prolyl-4 hydroxylase (P4H) type I from green algae… · 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
- Elsewhere: RCSB PDB 2V4A · PDBe 2V4A
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