Research workbench
Crystal structure of the beta-porphyranase BPGH16B (BACPLE_01689) from the human gut bacterium bacteroides plebeius
Analyse Crystal structure of the beta-porphyranase BPGH16B (BACPLE_01689) from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AWD
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-porphyranase
- EC
- 3.2.1.178
- UniProt
- B5CY92
- Ligands
- CA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-porphyranase (EC 3.2.1.178) | protein | 297 | 7% helix, 44% strand | B5CY92 |
| B | Beta-porphyranase (EC 3.2.1.178) | protein | 292 | 8% helix, 44% strand | B5CY92 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.74 | 0.80 | 63 | GOL |
| 2 | 693 | 0.74 | 0.80 | 61 | empty |
| 3 | 51 | 0.32 | 0.77 | 14 | GOL |
| 4 | 51 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4AWD · Crystal structure of the beta-porphyranase BpGH16B (BACPLE_01689) from the human gut… · the same entry in another collection · chain A against A, TM-score 1.00
- B5CY92 · AlphaFold monomer V2.0 prediction for beta-porphyranase B (B5CY92) · a predicted model of the same protein · chain B 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 B5CY92
- Elsewhere: RCSB PDB 4AWD · PDBe 4AWD · UniProt B5CY92
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