MolNFT v1 · #104456 · protein
Structure of modular XYN30D from paenibacillus barcinonensis
4QAW: “Structure of modular XYN30D from paenibacillus barcinonensis”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.75). MolNFT v1 #104456 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QAW
- Type
- protein
- Length
- 4,257 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- XYN30D
- EC
- 3.2.1.8
- UniProt
- H6WCZ0
- Ligands
- CA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | XYN30D (EC 3.2.1.8) | protein | 537 | 19% helix, 39% strand | H6WCZ0 |
| B | XYN30D (EC 3.2.1.8) | protein | 533 | 19% helix, 38% strand | H6WCZ0 |
| C | XYN30D (EC 3.2.1.8) | protein | 532 | 20% helix, 39% strand | H6WCZ0 |
| D, F, G | XYN30D (EC 3.2.1.8) | protein | 531 | 18% helix, 40% strand | H6WCZ0 |
| E | XYN30D (EC 3.2.1.8) | protein | 529 | 20% helix, 40% strand | H6WCZ0 |
| H | XYN30D (EC 3.2.1.8) | protein | 533 | 19% helix, 39% strand | H6WCZ0 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.75 | 0.78 | 109 | empty |
| 2 | 837 | 0.75 | 0.79 | 97 | empty |
| 3 | 774 | 0.70 | 0.77 | 77 | empty |
| 4 | 346 | 0.65 | 0.80 | 55 | empty |
| 5 | 274 | 0.64 | 0.81 | 41 | empty |
Interfaces
7 interfaces between chains.
- B–E · 1089 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1021 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 1006 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 269 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QAW · Structure of modular Xyn30D from Paenibacillus barci nsis · 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 H6WCZ0
- Elsewhere: RCSB PDB 4QAW · PDBe 4QAW · UniProt H6WCZ0
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