MolNFT v1 · #59603 · protein
Structure of the two subsite D-xylosidase from selenomonas ruminantium in complex with 1,3-BIS[TRIS(HYDROXYMETHYL)METHYLAMINO]PROPANE
3C2U · XYLOSIDASE/ARABINOSIDASE: “Structure of the two subsite D-xylosidase from selenomonas ruminantium in complex with…”. X-ray diffraction, 20 pockets (best druggability 0.77). MolNFT v1 #59603 on GenesisL1: 3D structure, binding sites…
- PDB
- 3C2U
- Type
- protein
- Length
- 2,149 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- XYLOSIDASE/ARABINOSIDASE
- UniProt
- O52575
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | XYLOSIDASE/ARABINOSIDASE | protein | 538 | 1% helix, 45% strand | O52575 |
| B, C, D | XYLOSIDASE/ARABINOSIDASE | protein | 537 | 1% helix, 45% strand | O52575 |
Ligands and binding sites
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.77 | 0.83 | 44 | empty |
| 2 | 683 | 0.76 | 0.82 | 44 | empty |
| 3 | 943 | 0.76 | 0.79 | 101 | B3P |
| 4 | 915 | 0.76 | 0.79 | 100 | B3P |
| 5 | 276 | 0.64 | 0.81 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2094 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2093 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1095 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1091 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3C2U · Structure of the two subsite D-xylosidase from Selenomonas ruminantium in complex with… · 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 O52575
- Elsewhere: RCSB PDB 3C2U · PDBe 3C2U · UniProt O52575
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