MolNFT v1 · #103781 · protein
Crystal structure of a nigd-like protein (BACCAC_02139) from bacteroides caccae atcc 43185 at 2.39 a resolution
4PQX · Uncharacterized protein: “Crystal structure of a nigd-like protein (BACCAC_02139) from bacteroides caccae atcc 43185 at 2.39 a…”. X-ray diffraction, 9 pockets (best druggability 0.78). MolNFT v1 #103781 on GenesisL1: 3D structure…
- PDB
- 4PQX
- Type
- protein
- Length
- 798 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A5ZGW9
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 201 | 7% helix, 48% strand | A5ZGW9 |
| B, D | Uncharacterized protein | protein | 199 | 8% helix, 49% strand | A5ZGW9 |
| C | Uncharacterized protein | protein | 199 | 8% helix, 48% strand | A5ZGW9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B, D, C
- IPA · Isopropyl alcohol · additive · 5 copies · chains A, C, D
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.78 | 0.81 | 56 | EDO, GOL |
| 2 | 880 | 0.77 | 0.80 | 62 | EDO |
| 3 | 929 | 0.77 | 0.80 | 66 | EDO, IPA |
| 4 | 139 | 0.40 | 0.74 | 21 | IPA |
| 5 | 109 | 0.35 | 0.73 | 20 | EDO |
Interfaces
4 interfaces between chains.
- B–C · 659 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 653 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 645 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 78 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4PQX · Crystal structure of a NigD-like protein (BACCAC_02139) from Bacteroides caccae ATCC… · 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 A5ZGW9
- Elsewhere: RCSB PDB 4PQX · PDBe 4PQX · UniProt A5ZGW9
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