MolNFT v1 · #121235 · protein
Crystal structures of rida in complex with pyruvate
5HP8 · Reactive intermediate deaminase a, chloroplastic: “Crystal structures of rida in complex with pyruvate”. X-ray diffraction, 1 ligand (PYR), 5 pockets (best druggability 0.73). MolNFT v1 #121235 on GenesisL1: 3D structure, binding…
- PDB
- 5HP8
- Type
- protein
- Length
- 324 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reactive intermediate deaminase a, chloroplastic
- EC
- 3.5.99.10
- UniProt
- Q94JQ4
- Ligands
- PYR
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Reactive intermediate deaminase a, chloroplastic (EC 3.5.99.10) | protein | 108 | 32% helix, 33% strand | Q94JQ4 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.73 | 0.98 | 23 | empty |
| 2 | 219 | 0.51 | 0.76 | 26 | PYR |
| 3 | 206 | 0.48 | 0.75 | 21 | PYR |
| 4 | 214 | 0.48 | 0.75 | 25 | PYR |
| 5 | 60 | 0.43 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 703 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 702 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 688 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5HP8 · Crystal structures of RidA in complex with pyruvate · the same entry in another collection · chain A against A, TM-score 1.00
- Q94JQ4 · AlphaFold monomer V2.0 prediction for reactive intermediate deaminase a, chloroplastic… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q94JQ4
- Elsewhere: RCSB PDB 5HP8 · PDBe 5HP8 · UniProt Q94JQ4
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