MolNFT v1 · #104608 · protein
Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from bacteroides vulgatus atcc 8482 at 1.90 a resolution
4QFU: “Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from bacteroides vulgatus atcc 8482 at 1.90 a…”. X-ray diffraction, 3 ligands (SAR, CL, NO3), 20 pockets (best druggability 0.78). MolNFT v1 #104608 on GenesisL1: 3D…
- PDB
- 4QFU
- Type
- protein
- Length
- 5,563 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 5
- UniProt
- A6L3N2
- Ligands
- SAR, CL, NO3
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 9 distinct chains · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase family 5 | protein | 461 | 27% helix, 21% strand | A6L3N2 |
| B | Glycoside hydrolase family 5 | protein | 468 | 27% helix, 20% strand | A6L3N2 |
| C | Glycoside hydrolase family 5 | protein | 459 | 27% helix, 22% strand | A6L3N2 |
| D | Glycoside hydrolase family 5 | protein | 458 | 27% helix, 22% strand | A6L3N2 |
| E | Glycoside hydrolase family 5 | protein | 472 | 26% helix, 20% strand | A6L3N2 |
| F | Glycoside hydrolase family 5 | protein | 465 | 27% helix, 20% strand | A6L3N2 |
| G, I | Glycoside hydrolase family 5 | protein | 465 | 27% helix, 21% strand | A6L3N2 |
| H | Glycoside hydrolase family 5 | protein | 461 | 27% helix, 22% strand | A6L3N2 |
| J, K, L | Glycoside hydrolase family 5 | protein | 463 | 27% helix, 21% strand | A6L3N2 |
Ligands and binding sites
- SAR · Sarcosine · ligand · 3 copies · chains C, G, K
- CL · Chloride ion · ion · 12 copies · chains A, B, H, C, D, E, F, G, I, J, K, L
- NO3 · Nitrate ion · ion · 3 copies · chains B, G, C, E, F, H
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 24 copies · chains A, B, C, E, D, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.78 | 0.86 | 50 | empty |
| 2 | 419 | 0.77 | 0.86 | 49 | empty |
| 3 | 373 | 0.76 | 0.87 | 47 | empty |
| 4 | 939 | 0.76 | 0.79 | 80 | empty |
| 5 | 511 | 0.75 | 0.83 | 63 | empty |
Interfaces
22 interfaces between chains.
- C–E · 1039 Ų buried · 11 hydrogen bonds · protein-protein
- B–G · 967 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 940 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 741 Ų buried · 8 hydrogen bonds · protein-protein
- B–I · 739 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 168 modified (engineered).
Compared structures
- 4QFU · Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus… · the same entry in another collection · chain H against H, 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 A6L3N2
- Elsewhere: RCSB PDB 4QFU · PDBe 4QFU · UniProt A6L3N2
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