Research workbench
Structure of paenibacillus xanthan lyase to 2.6 a resolution
Analyse Structure of paenibacillus xanthan lyase to 2.6 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F2P
- Type
- protein
- Length
- 1,040 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paenibacillus xanthan lyase
- EC
- 4.2.2.12
- Ligands
- CA, CL
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Paenibacillus xanthan lyase (EC 4.2.2.12) | protein | 1040 | 24% helix, 33% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 17 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.71 | 0.76 | 61 | MRD, MPD |
| 2 | 188 | 0.48 | 0.76 | 38 | MRD, MPD |
| 3 | 50 | 0.45 | 0.85 | 17 | CA |
| 4 | 85 | 0.35 | 0.75 | 19 | CA |
| 5 | 75 | 0.31 | 0.74 | 18 | empty |
Compared structures
- 6F2P · Structure of Paenibacillus xanthan lyase to 2.6 A resolution · 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
- Elsewhere: RCSB PDB 6F2P · PDBe 6F2P
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