MolNFT v1 · #168305 · protein
2.52 ångström resolution crystal structure of 6-phospho-alpha- glucosidase from gut microorganisms in complex with NAD and glucose- 6-phosphate
6WBT · Cellulase IBT99: “2.52 ångström resolution crystal structure of 6-phospho-alpha- glucosidase from gut microorganisms in complex…”. X-ray diffraction, 4 ligands (NAD, G6P, MN), 16 pockets (best druggability 0.82). MolNFT v1 #168305…
- PDB
- 6WBT
- Type
- protein
- Length
- 1,751 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulase IBT99
- Ligands
- NAD, G6P, MN, PO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulase IBT99 | protein | 442 | 49% helix, 17% strand | — |
| B | Cellulase IBT99 | protein | 440 | 50% helix, 17% strand | — |
| C | Cellulase IBT99 | protein | 441 | 50% helix, 17% strand | — |
| D | Cellulase IBT99 | protein | 428 | 48% helix, 17% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 3 copies · chains A, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.82 | 0.85 | 86 | MN, G6P, NAD |
| 2 | 1076 | 0.82 | 0.83 | 115 | G6P, NAD |
| 3 | 735 | 0.81 | 0.85 | 86 | MN, PO4, NAD |
| 4 | 747 | 0.76 | 0.81 | 75 | MN, G6P, NAD |
| 5 | 481 | 0.67 | 0.78 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1688 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1653 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 931 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 911 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 6WBT · 2.52 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Gut… · 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 6WBT · PDBe 6WBT
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