Research workbench
Structure of dpp III from caldithrix abyssi
Analyse Structure of dpp III from caldithrix abyssi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EOM
- Type
- protein
- Length
- 526 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MUTT/NUDIX family protein
- UniProt
- H1XW48
- Ligands
- ZN, NA, CL
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MUTT/NUDIX family protein | protein | 526 | 55% helix, 15% strand | H1XW48 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.77 | 0.79 | 88 | empty |
| 2 | 138 | 0.51 | 0.79 | 21 | empty |
| 3 | 64 | 0.33 | 0.75 | 14 | empty |
Compared structures
- 6EOM · Structure of DPP III from Caldithrix abyssi · 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 H1XW48
- Elsewhere: RCSB PDB 6EOM · PDBe 6EOM · UniProt H1XW48
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