Research workbench
Crystal structure analysis of recombinant rat kidney long- chain hydroxy acid oxidase
Analyse Crystal structure analysis of recombinant rat kidney long- chain hydroxy acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TB3
- Type
- protein
- Length
- 2,637 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxyacid oxidase 3
- EC
- 1.1.3.15
- UniProt
- Q07523
- Ligands
- FMN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, H | Hydroxyacid oxidase 3 (EC 1.1.3.15) | protein | 332 | 45% helix, 13% strand | Q07523 |
| B | Hydroxyacid oxidase 3 (EC 1.1.3.15) | protein | 327 | 46% helix, 13% strand | Q07523 |
| D | Hydroxyacid oxidase 3 (EC 1.1.3.15) | protein | 329 | 46% helix, 13% strand | Q07523 |
| E | Hydroxyacid oxidase 3 (EC 1.1.3.15) | protein | 324 | 46% helix, 13% strand | Q07523 |
| G | Hydroxyacid oxidase 3 (EC 1.1.3.15) | protein | 329 | 46% helix, 13% strand | Q07523 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ACY · Acetic acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.78 | 0.84 | 76 | FMN, ACY |
| 2 | 575 | 0.78 | 0.84 | 76 | FMN, ACY |
| 3 | 491 | 0.78 | 0.85 | 67 | FMN, ACY |
| 4 | 470 | 0.78 | 0.86 | 63 | FMN, ACY |
| 5 | 489 | 0.77 | 0.85 | 66 | FMN, ACY |
Interfaces
12 interfaces between chains.
- A–D · 1453 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1449 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1445 Ų buried · 16 hydrogen bonds · protein-protein
- E–G · 1441 Ų buried · 17 hydrogen bonds · protein-protein
- F–H · 1433 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1TB3 · Crystal Structure Analysis of Recombinant Rat Kidney Long-chain Hydroxy Acid Oxidase · the same entry in another collection · chain H against H, TM-score 1.00
- Q07523 · AlphaFold monomer V2.0 prediction for hydroxyacid oxidase 2 (Q07523) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q07523
- Elsewhere: RCSB PDB 1TB3 · PDBe 1TB3 · UniProt Q07523
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