MolNFT v1 · #104681 · protein
Crystal structure of a putative glycosyl hydrolase (BDI_3914) from parabacteroides distasonis atcc 8503 at 2.13 a resolution
4QHZ: “Crystal structure of a putative glycosyl hydrolase (BDI_3914) from parabacteroides distasonis atcc 8503 at…”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.75). MolNFT v1 #104681 on GenesisL1: 3D structure…
- PDB
- 4QHZ
- Type
- protein
- Length
- 952 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycosyl hydrolase
- UniProt
- A6LIT1
- Ligands
- MG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative glycosyl hydrolase | protein | 236 | 6% helix, 35% strand | A6LIT1 |
| C, D | Putative glycosyl hydrolase | protein | 240 | 5% helix, 34% strand | A6LIT1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.75 | 0.88 | 40 | EDO |
| 2 | 187 | 0.73 | 0.89 | 33 | empty |
| 3 | 50 | 0.69 | 0.98 | 23 | EDO |
| 4 | 82 | 0.59 | 0.88 | 20 | empty |
| 5 | 71 | 0.33 | 0.75 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2526 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2517 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 548 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 547 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 459 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (methylation, engineered).
Compared structures
- 4QHZ · Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides… · 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
- Every structure of UniProt A6LIT1
- Elsewhere: RCSB PDB 4QHZ · PDBe 4QHZ · UniProt A6LIT1
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