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Crystal structure of alpha-neoagarobiose hydrolase (alpha-nabh) in complex with alpha-D-galactopyranose from saccharophagus degradans 2- 40
Analyse Crystal structure of alpha-neoagarobiose hydrolase (alpha-nabh) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R4Z
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 32, N terminal
- EC
- 3.2.1.-
- UniProt
- Q21HB2
- Ligands
- GLA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 32, N terminal (EC 3.2.1.-) | protein | 358 | 4% helix, 43% strand | Q21HB2 |
| B | Glycosyl hydrolase family 32, N terminal (EC 3.2.1.-) | protein | 359 | 4% helix, 43% strand | Q21HB2 |
Ligands and binding sites
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.81 | 0.97 | 34 | GLA |
| 2 | 153 | 0.81 | 0.97 | 32 | GLA |
| 3 | 440 | 0.68 | 0.80 | 51 | empty |
| 4 | 125 | 0.42 | 0.75 | 23 | empty |
| 5 | 109 | 0.41 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3249 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 3R4Z · Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) in complex with… · 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 Q21HB2
- Elsewhere: RCSB PDB 3R4Z · PDBe 3R4Z · UniProt Q21HB2
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