MolNFT v1 · #97522 · protein
Crystal structure of human alpha-L-iduronidase complex with [2R,3R,4R, 5S]-2-carboxy-3,4,5-trihydroxy-piperidine
4KGL: “Crystal structure of human alpha-L-iduronidase complex with [2R,3R,4R…”. X-ray diffraction, 4 ligands (IDJ, NAG, MAN), 12 pockets (best druggability 0.67). MolNFT v1 #97522 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4KGL
- Type
- protein
- Length
- 1,207 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-iduronidase
- EC
- 3.2.1.76
- UniProt
- P35475
- Ligands
- IDJ, NAG, MAN, BMA
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-L-iduronidase (EC 3.2.1.76) | protein | 595 | 25% helix, 31% strand | P35475 |
| B | Alpha-L-iduronidase (EC 3.2.1.76) | protein | 612 | 25% helix, 30% strand | P35475 |
Ligands and binding sites
- IDJ · (2R,3R,4R,5S)-3,4,5-trihydroxypiperidine-2-carboxylic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.67 | 0.77 | 79 | NAG, GOL |
| 2 | 62 | 0.64 | 0.93 | 18 | empty |
| 3 | 153 | 0.57 | 0.82 | 19 | empty |
| 4 | 144 | 0.54 | 0.81 | 21 | empty |
| 5 | 147 | 0.49 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 275 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
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 P35475
- Elsewhere: RCSB PDB 4KGL · PDBe 4KGL · UniProt P35475
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