Research workbench
Crystal structure of nudix hydrolase ORF153, ymfb, from escherichia COLI K-1
Analyse Crystal structure of nudix hydrolase ORF153, ymfb, from escherichia COLI K-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SHD
- Type
- protein
- Length
- 1,800 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatase nudj
- EC
- 3.6.1.-
- UniProt
- A1AA28
- Ligands
- MN, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Phosphatase nudj (EC 3.6.1.-) | protein | 150 | 22% helix, 35% strand | A1AA28 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 36 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.85 | 0.86 | 162 | empty |
| 2 | 954 | 0.79 | 0.81 | 71 | empty |
| 3 | 819 | 0.74 | 0.79 | 65 | empty |
| 4 | 797 | 0.74 | 0.79 | 53 | empty |
| 5 | 400 | 0.74 | 0.84 | 58 | empty |
Interfaces
26 interfaces between chains.
- F–K · 1774 Ų buried · 21 hydrogen bonds · protein-protein
- C–G · 1741 Ų buried · 21 hydrogen bonds · protein-protein
- A–I · 1719 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1712 Ų buried · 17 hydrogen bonds · protein-protein
- B–L · 1709 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3SHD · Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1 · the same entry in another collection · chain L against L, 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 A1AA28
- Elsewhere: RCSB PDB 3SHD · PDBe 3SHD · UniProt A1AA28
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