MolNFT v1 · #156520 · protein
Amylomaltase from streptococcus agalactiae in complex with acarbose
6M6T · 4-alpha-glucanotransferase: “Amylomaltase from streptococcus agalactiae in complex with acarbose”. X-ray diffraction, 3 ligands (AC1, ASO, GLC), 20 pockets (best druggability 0.83). MolNFT v1 #156520 on GenesisL1: 3D structure…
- PDB
- 6M6T
- Type
- protein
- Length
- 3,974 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-alpha-glucanotransferase
- EC
- 2.4.1.25
- UniProt
- A0A0E1EIJ0
- Ligands
- AC1, ASO, GLC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 496 | 43% helix, 13% strand | A0A0E1EIJ0 |
| B | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 497 | 43% helix, 13% strand | A0A0E1EIJ0 |
| C | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 499 | 44% helix, 13% strand | A0A0E1EIJ0 |
| D, F | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 496 | 44% helix, 13% strand | A0A0E1EIJ0 |
| E | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 497 | 46% helix, 13% strand | A0A0E1EIJ0 |
| G | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 498 | 45% helix, 12% strand | A0A0E1EIJ0 |
| H | 4-alpha-glucanotransferase (EC 2.4.1.25) | protein | 495 | 42% helix, 14% strand | A0A0E1EIJ0 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- ASO · 1,5-anhydro-D-glucitol · ligand · 7 copies · chains A, B, C, D, E, F, H
- GLC · alpha-D-glucopyranose · sugar · 12 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.83 | 0.98 | 24 | empty |
| 2 | 938 | 0.83 | 0.84 | 96 | empty |
| 3 | 158 | 0.83 | 0.98 | 23 | empty |
| 4 | 166 | 0.83 | 0.98 | 25 | empty |
| 5 | 939 | 0.82 | 0.83 | 95 | empty |
Interfaces
15 interfaces between chains.
- E–H · 1324 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 1180 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1171 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1167 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1089 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 6M6T · Amylomaltase from Streptococcus agalactiae in complex with acarbose · 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 A0A0E1EIJ0
- Elsewhere: RCSB PDB 6M6T · PDBe 6M6T · UniProt A0A0E1EIJ0
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