MolNFT v1 · #58781 · protein
Crystal structure of a putative yden-like hydrolase (ECA3091) from pectobacterium atrosepticum SCRI1043 at 1.66 a resolution
3BDV · Uncharacterized protein DUF1234: “Crystal structure of a putative yden-like hydrolase (ECA3091) from pectobacterium atrosepticum SCRI1043 at…”. X-ray diffraction, 2 ligands (CA, CL), 5 pockets (best druggability 0.46). MolNFT v1…
- PDB
- 3BDV
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein DUF1234
- UniProt
- Q6D2K4
- Ligands
- CA, CL
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein DUF1234 | protein | 191 | 39% helix, 16% strand | Q6D2K4 |
| B | Uncharacterized protein DUF1234 | protein | 185 | 39% helix, 16% strand | Q6D2K4 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.46 | 0.77 | 20 | empty |
| 2 | 123 | 0.44 | 0.77 | 18 | empty |
| 3 | 90 | 0.39 | 0.76 | 15 | empty |
| 4 | 73 | 0.36 | 0.77 | 17 | CL |
| 5 | 63 | 0.32 | 0.76 | 16 | CL |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3BDV · Crystal structure of a putative yden-like hydrolase (eca3091) from pectobacterium… · the same entry in another collection · chain B against B, 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 Q6D2K4
- Elsewhere: RCSB PDB 3BDV · PDBe 3BDV · UniProt Q6D2K4
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