MolNFT v1 · #100031 · protein
Structure of RS223-beta-xylosidase
4MLG: “Structure of RS223-beta-xylosidase”. X-ray diffraction, 2 ligands (CA, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #100031 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4MLG
- Type
- protein
- Length
- 3,875 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylosidase
- EC
- 3.2.1.37
- UniProt
- I7EUE2
- Ligands
- CA, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, J | Beta-xylosidase (EC 3.2.1.37) | protein | 323 | 4% helix, 43% strand | I7EUE2 |
| D, L | Beta-xylosidase (EC 3.2.1.37) | protein | 322 | 4% helix, 43% strand | I7EUE2 |
| G, H, K | Beta-xylosidase (EC 3.2.1.37) | protein | 324 | 3% helix, 41% strand | I7EUE2 |
| I | Beta-xylosidase (EC 3.2.1.37) | protein | 321 | 3% helix, 43% strand | I7EUE2 |
Ligands and binding sites
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.79 | 0.81 | 62 | empty |
| 2 | 90 | 0.77 | 0.98 | 20 | empty |
| 3 | 74 | 0.74 | 0.98 | 20 | empty |
| 4 | 802 | 0.74 | 0.79 | 72 | SO4 |
| 5 | 1103 | 0.72 | 0.76 | 78 | empty |
Interfaces
21 interfaces between chains.
- E–F · 1136 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 1132 Ų buried · 24 hydrogen bonds · protein-protein
- K–L · 1128 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1124 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1115 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4MLG · Structure of RS223-Beta-xylosidase · 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 I7EUE2
- Elsewhere: RCSB PDB 4MLG · PDBe 4MLG · UniProt I7EUE2
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