Research workbench
Crystal structure of abp-wt, a GH27-B-L-arabinopyranosidase from geobacillus stearothermophilus
Analyse Crystal structure of abp-wt, 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
- 4NX0
- Type
- protein
- Length
- 3,446 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Abp, a GH27 beta-L-arabinopyranosidase
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, H | Abp, a GH27 beta-L-arabinopyranosidase | protein | 430 | 32% helix, 25% strand | — |
| C | Abp, a GH27 beta-L-arabinopyranosidase | protein | 431 | 32% helix, 25% strand | — |
| D | Abp, a GH27 beta-L-arabinopyranosidase | protein | 435 | 33% helix, 24% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 85 copies · chains A, E, B, C, H, D, G, F
- GOL · Glycerol · additive · 40 copies · chains A, E, B, C, G, D, F, H
- CIT · Citric acid · additive · 5 copies · chains A, B, C, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.75 | 0.78 | 94 | GOL, SO4 |
| 2 | 472 | 0.65 | 0.78 | 47 | SO4 |
| 3 | 490 | 0.63 | 0.76 | 51 | SO4 |
| 4 | 443 | 0.60 | 0.75 | 34 | SO4 |
| 5 | 396 | 0.59 | 0.75 | 33 | SO4 |
Interfaces
13 interfaces between chains.
- G–H · 856 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 852 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 820 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 811 Ų buried · 7 hydrogen bonds · protein-protein
- E–G · 810 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4NX0 · Crystal structure of Abp-WT, 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 4NX0 · PDBe 4NX0
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