Research workbench
Crystal structure of putative glycosyl hydrolase (YP_001301887.1) from parabacteroides distasonis atcc 8503 at 2.00 a resolution
Analyse Crystal structure of putative glycosyl hydrolase (YP_001301887.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IMM
- Type
- protein
- Length
- 591 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative secreted glycosylhydrolase
- UniProt
- A6L9A1
- Ligands
- NA, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative secreted glycosylhydrolase | protein | 197 | 6% helix, 41% strand | A6L9A1 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.77 | 0.82 | 76 | CL |
| 2 | 666 | 0.75 | 0.81 | 76 | TRS |
| 3 | 83 | 0.51 | 0.84 | 17 | empty |
| 4 | 95 | 0.43 | 0.79 | 23 | empty |
Interfaces
2 interfaces between chains.
- B–C · 570 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 555 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3IMM · Crystal structure of Putative glycosyl hydrolase (YP_001301887.1) from Parabacteroides… · 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 A6L9A1
- Elsewhere: RCSB PDB 3IMM · PDBe 3IMM · UniProt A6L9A1
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