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The structure of ycao from methanopyrus kandleri bound with amppcp and MG2+
Analyse The structure of ycao from methanopyrus kandleri bound with amppcp and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CI7
- Type
- protein
- Length
- 2,178 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ycao
- UniProt
- Q8TZ25
- Ligands
- ACP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ycao | protein | 365 | 33% helix, 23% strand | Q8TZ25 |
| B, E | Ycao | protein | 364 | 33% helix, 23% strand | Q8TZ25 |
| C | Ycao | protein | 361 | 34% helix, 24% strand | Q8TZ25 |
| D | Ycao | protein | 362 | 34% helix, 23% strand | Q8TZ25 |
| F | Ycao | protein | 362 | 34% helix, 23% strand | Q8TZ25 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.82 | 0.84 | 82 | ACP, MG |
| 2 | 967 | 0.82 | 0.83 | 85 | ACP, MG |
| 3 | 834 | 0.80 | 0.83 | 75 | ACP, MG |
| 4 | 988 | 0.80 | 0.81 | 83 | ACP, MG |
| 5 | 687 | 0.77 | 0.82 | 81 | ACP, MG |
Interfaces
7 interfaces between chains.
- A–F · 595 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 579 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 506 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 477 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 422 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 6CI7 · The structure of YcaO from Methanopyrus kandleri bound with AMPPCP and Mg2+ · 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 Q8TZ25
- Elsewhere: RCSB PDB 6CI7 · PDBe 6CI7 · UniProt Q8TZ25
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