MolNFT v1 · #127312 · protein
Glycoside hydrolase BT_3662
5MSX · Putative endo-1,4-beta-xylanase: “Glycoside hydrolase BT_3662”. X-ray diffraction, 1 ligand (CA), 18 pockets (best druggability 0.77). MolNFT v1 #127312 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MSX
- Type
- protein
- Length
- 1,318 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative endo-1,4-beta-xylanase
- UniProt
- Q8A1J9
- Ligands
- CA
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative endo-1,4-beta-xylanase | protein | 439 | 4% helix, 43% strand | Q8A1J9 |
| C | Putative endo-1,4-beta-xylanase | protein | 440 | 4% helix, 43% strand | Q8A1J9 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, C, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.77 | 0.79 | 100 | EDO |
| 2 | 607 | 0.69 | 0.78 | 39 | EDO |
| 3 | 373 | 0.59 | 0.76 | 26 | empty |
| 4 | 119 | 0.54 | 0.83 | 25 | empty |
| 5 | 120 | 0.52 | 0.81 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 424 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 369 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5MSX · Glycoside hydrolase BT_3662 · 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 Q8A1J9
- Elsewhere: RCSB PDB 5MSX · PDBe 5MSX · UniProt Q8A1J9
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