Research workbench
Crystal structure of abp-D197A (a GH27-B-L-arabinopyranosidase from geobacillus stearothermophilus), in complex with arabinose
Analyse Crystal structure of abp-D197A (a GH27-B-L-arabinopyranosidase from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NZF
- Type
- protein
- Length
- 3,450 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abp, a GH27 beta-L-arabinopyranosidase
- Ligands
- ARB, SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Abp, a GH27 beta-L-arabinopyranosidase | protein | 431 | 32% helix, 25% strand | — |
| B, F, H | Abp, a GH27 beta-L-arabinopyranosidase | protein | 430 | 32% helix, 24% strand | — |
| C | Abp, a GH27 beta-L-arabinopyranosidase | protein | 432 | 33% helix, 25% strand | — |
| D | Abp, a GH27 beta-L-arabinopyranosidase | protein | 435 | 32% helix, 25% strand | — |
Ligands and binding sites
- ARB · beta-L-arabinopyranose · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 82 copies · chains A, E, B, C, G, D, H, F
- GOL · Glycerol · additive · 20 copies · chains A, B, E, C, D, H, F, G
- CIT · Citric acid · additive · 6 copies · chains A, B, C, D, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.72 | 0.76 | 90 | SO4 |
| 2 | 842 | 0.70 | 0.76 | 83 | empty |
| 3 | 684 | 0.69 | 0.77 | 71 | SO4 |
| 4 | 445 | 0.61 | 0.76 | 49 | GOL, SO4 |
| 5 | 557 | 0.61 | 0.74 | 67 | SO4, GOL |
Interfaces
13 interfaces between chains.
- G–H · 877 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 834 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 825 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 817 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 816 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4NZF · Crystal structure of Abp-D197A (a GH27-b-L-arabinopyranosidase from Geobacillus… · 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
- Elsewhere: RCSB PDB 4NZF · PDBe 4NZF
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