MolNFT v1 · #157020 · protein
Bifunctional GH43-ce bacteroides eggerthii, BACEGG_01304
6MLY · Bifunctional GH43-ce protein: “Bifunctional GH43-ce bacteroides eggerthii, BACEGG_01304”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.74). MolNFT v1 #157020 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6MLY
- Type
- protein
- Length
- 3,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional GH43-ce protein
- EC
- 3.2.1.37
- UniProt
- A0A380YKU1
- Ligands
- NA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional GH43-ce protein (EC 3.2.1.37) | protein | 711 | 14% helix, 37% strand | A0A380YKU1 |
| B, D | Bifunctional GH43-ce protein (EC 3.2.1.37) | protein | 772 | 14% helix, 39% strand | A0A380YKU1 |
| C | Bifunctional GH43-ce protein (EC 3.2.1.37) | protein | 774 | 13% helix, 39% strand | A0A380YKU1 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.74 | 0.77 | 111 | EDO |
| 2 | 966 | 0.73 | 0.77 | 104 | empty |
| 3 | 175 | 0.60 | 0.82 | 22 | empty |
| 4 | 243 | 0.57 | 0.78 | 21 | empty |
| 5 | 119 | 0.56 | 0.84 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–C · 304 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 269 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 128 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 111 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6MLY · Bifunctional GH43-CE Bacteroides eggerthii, BACEGG_01304 · 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 A0A380YKU1
- Elsewhere: RCSB PDB 6MLY · PDBe 6MLY · UniProt A0A380YKU1
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