Research workbench
Crystal structure of the pduu shell protein from the pdu microcompartment
Analyse Crystal structure of the pduu shell protein from the pdu microcompartment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CGI
- Type
- protein
- Length
- 460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propanediol utilization protein pduu
- UniProt
- P0A1D1
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Propanediol utilization protein pduu | protein | 112 | 32% helix, 37% strand | P0A1D1 |
| C | Propanediol utilization protein pduu | protein | 119 | 31% helix, 34% strand | P0A1D1 |
| D | Propanediol utilization protein pduu | protein | 117 | 31% helix, 33% strand | P0A1D1 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.41 | 0.73 | 27 | empty |
| 2 | 77 | 0.32 | 0.74 | 15 | empty |
| 3 | 52 | 0.26 | 0.73 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1495 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1422 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 379 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3CGI · Crystal structure of the PduU shell protein from the Pdu microcompartment · the same entry in another collection · chain A against A, TM-score 1.00
- P0A1D1 · AlphaFold monomer V2.0 prediction for propanediol utilization protein pduu (P0A1D1) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P0A1D1
- Elsewhere: RCSB PDB 3CGI · PDBe 3CGI · UniProt P0A1D1
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