MolNFT v1 · #69258 · protein
Crystal structure of ligand bound xync
3KL3 · Glucuronoxylanase xync: “Crystal structure of ligand bound xync”. X-ray diffraction, 3 ligands (DHI, GCU, BDP), 13 pockets (best druggability 0.83). MolNFT v1 #69258 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KL3
- Type
- protein
- Length
- 1,537 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucuronoxylanase xync
- EC
- 3.2.1.136
- UniProt
- Q45070
- Ligands
- DHI, GCU, BDP
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucuronoxylanase xync (EC 3.2.1.136) | protein | 389 | 25% helix, 32% strand | Q45070 |
| B | Glucuronoxylanase xync (EC 3.2.1.136) | protein | 390 | 26% helix, 34% strand | Q45070 |
| C | Glucuronoxylanase xync (EC 3.2.1.136) | protein | 390 | 26% helix, 33% strand | Q45070 |
| D | Glucuronoxylanase xync (EC 3.2.1.136) | protein | 368 | 25% helix, 30% strand | Q45070 |
Ligands and binding sites
- DHI · D-histidine · ligand · 2 copies · chains A, B
- GCU · alpha-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · chains B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.83 | 0.84 | 147 | empty |
| 2 | 796 | 0.70 | 0.76 | 77 | empty |
| 3 | 528 | 0.68 | 0.78 | 49 | empty |
| 4 | 255 | 0.57 | 0.78 | 31 | empty |
| 5 | 117 | 0.46 | 0.78 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–C · 851 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 612 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 469 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 Q45070
- Elsewhere: RCSB PDB 3KL3 · PDBe 3KL3 · UniProt Q45070
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