Research workbench
Crystal structure of a DUF1329 family protein (DESPIG_00262) from desulfovibrio piger atcc 29098 at 1.75 a resolution
Analyse Crystal structure of a DUF1329 family protein (DESPIG_00262) from desulfovibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z48
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- B6WQE2
- Ligands
- NA, IOD, CL
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein | protein | 240 | 13% helix, 53% strand | B6WQE2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
- IOD · Iodide ion · ion · 7 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.87 | 0.90 | 79 | empty |
| 2 | 697 | 0.87 | 0.91 | 63 | 1PE |
| 3 | 250 | 0.54 | 0.77 | 40 | IOD |
Interfaces
1 interface between chains.
- A–B · 492 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4Z48 · Crystal structure of a DUF1329 family protein (DESPIG_00262) from Desulfovibrio piger… · 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 B6WQE2
- Elsewhere: RCSB PDB 4Z48 · PDBe 4Z48 · UniProt B6WQE2
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