Research workbench
Crystal structure of macrocyclase amdnb from anabaena sp. pcc 7120
Analyse Crystal structure of macrocyclase amdnb from anabaena sp. pcc 7120 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M4S
- Type
- protein
- Length
- 1,214 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amdnb protein
- UniProt
- Q8YLC3
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amdnb protein | protein | 311 | 34% helix, 31% strand | Q8YLC3 |
| B | Amdnb protein | protein | 314 | 32% helix, 29% strand | Q8YLC3 |
| C | Amdnb protein | protein | 297 | 33% helix, 29% strand | Q8YLC3 |
| D | Amdnb protein | protein | 292 | 32% helix, 29% strand | Q8YLC3 |
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.84 | 0.88 | 96 | empty |
| 2 | 1179 | 0.79 | 0.80 | 115 | empty |
| 3 | 219 | 0.68 | 0.86 | 24 | empty |
| 4 | 125 | 0.61 | 0.86 | 24 | empty |
| 5 | 168 | 0.58 | 0.82 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2706 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 2554 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 1372 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 215 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 214 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7M4S · Crystal structure of macrocyclase AMdnB from Anabaena sp. PCC 7120 · the same entry in another collection · chain B against B, 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 Q8YLC3
- Elsewhere: RCSB PDB 7M4S · PDBe 7M4S · UniProt Q8YLC3
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