Research workbench
Crystal structure of AMUC_1100 from akkermansia muciniphila
Analyse Crystal structure of AMUC_1100 from akkermansia muciniphila in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LAD
- Type
- protein
- Length
- 1,133 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMUC_1100
- UniProt
- B2UR41
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMUC_1100 | protein | 197 | 45% helix, 22% strand | B2UR41 |
| B | AMUC_1100 | protein | 184 | 48% helix, 22% strand | B2UR41 |
| C | AMUC_1100 | protein | 194 | 47% helix, 22% strand | B2UR41 |
| D | AMUC_1100 | protein | 190 | 45% helix, 22% strand | B2UR41 |
| E | AMUC_1100 | protein | 186 | 47% helix, 23% strand | B2UR41 |
| F | AMUC_1100 | protein | 182 | 46% helix, 23% strand | B2UR41 |
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.72 | 0.84 | 62 | empty |
| 2 | 1069 | 0.70 | 0.75 | 110 | empty |
| 3 | 1075 | 0.70 | 0.74 | 117 | empty |
| 4 | 615 | 0.65 | 0.75 | 75 | empty |
| 5 | 104 | 0.54 | 0.83 | 25 | empty |
Interfaces
12 interfaces between chains.
- A–C · 1047 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 989 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 979 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 922 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 861 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6LAD · Crystal structure of Amuc_1100 from Akkermansia muciniphila · the same entry in another collection · chain E against E, 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 B2UR41
- Elsewhere: RCSB PDB 6LAD · PDBe 6LAD · UniProt B2UR41
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