Research workbench
X-ray structure of an enterobacter GH43 beta-xylosidase: ECXYL43 F507A mutant
Analyse X-ray structure of an enterobacter GH43 beta-xylosidase: ECXYL43 F507A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K1R
- Type
- protein
- Length
- 2,133 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta xylosidase GH43
- EC
- 3.2.1.37
- UniProt
- V5J3M5
- Ligands
- CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 1% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta xylosidase GH43 (EC 3.2.1.37) | protein | 536 | 1% helix, 48% strand | V5J3M5 |
| B | Beta xylosidase GH43 (EC 3.2.1.37) | protein | 532 | 1% helix, 49% strand | V5J3M5 |
| C | Beta xylosidase GH43 (EC 3.2.1.37) | protein | 531 | 1% helix, 48% strand | V5J3M5 |
| D | Beta xylosidase GH43 (EC 3.2.1.37) | protein | 534 | 1% helix, 48% strand | V5J3M5 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
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 | 550 | 0.79 | 0.86 | 59 | empty |
| 2 | 945 | 0.75 | 0.78 | 69 | empty |
| 3 | 301 | 0.65 | 0.81 | 28 | empty |
| 4 | 310 | 0.65 | 0.81 | 28 | empty |
| 5 | 331 | 0.64 | 0.80 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1955 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 395 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 291 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 140 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7K1R · X-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 F507A mutant · 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 V5J3M5
- Elsewhere: RCSB PDB 7K1R · PDBe 7K1R · UniProt V5J3M5
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