MolNFT v1 · #108266 · protein
Structure of a selenomethionine derivative of the GH76 alpha-mannanase BT2949 bacteroides thetaiotaomicron
4V1R · Alpha-1,6-mannanase: “Structure of a selenomethionine derivative of the GH76 alpha-mannanase BT2949 bacteroides thetaiotaomicron”. X-ray diffraction, 1 ligand (SRT), 7 pockets (best druggability 0.61). MolNFT v1 #108266 on…
- PDB
- 4V1R
- Type
- protein
- Length
- 722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,6-mannanase
- EC
- 3.2.1.101
- UniProt
- Q8A3K5
- Ligands
- SRT
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-1,6-mannanase (EC 3.2.1.101) | protein | 361 | 61% helix, 9% strand | Q8A3K5 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.61 | 0.78 | 34 | empty |
| 2 | 207 | 0.54 | 0.78 | 29 | empty |
| 3 | 177 | 0.48 | 0.76 | 26 | empty |
| 4 | 149 | 0.46 | 0.76 | 25 | empty |
| 5 | 54 | 0.37 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 350 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4V1R · Structure of a selenomethionine derivative of the GH76 alpha- mannanase BT2949… · 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 Q8A3K5
- Elsewhere: RCSB PDB 4V1R · PDBe 4V1R · UniProt Q8A3K5
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