Research workbench
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
- 6CIB
- Type
- protein
- Length
- 2,170 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ycao
- UniProt
- Q8TZ25
- Ligands
- ADP, OXM, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ycao | protein | 363 | 34% helix, 24% strand | Q8TZ25 |
| B | Ycao | protein | 364 | 34% helix, 23% strand | Q8TZ25 |
| C | Ycao | protein | 360 | 35% helix, 24% strand | Q8TZ25 |
| D | Ycao | protein | 360 | 34% helix, 24% strand | Q8TZ25 |
| E | Ycao | protein | 361 | 34% helix, 24% strand | Q8TZ25 |
| F | Ycao | protein | 362 | 34% helix, 24% strand | Q8TZ25 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- OXM · Oxamic acid · ligand · 6 copies · chains A, B, E, C, D, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.81 | 0.82 | 75 | ADP, MG |
| 2 | 1108 | 0.80 | 0.82 | 90 | ADP, MG |
| 3 | 863 | 0.79 | 0.82 | 73 | ADP, MG |
| 4 | 821 | 0.79 | 0.82 | 75 | ADP, MG |
| 5 | 986 | 0.79 | 0.80 | 74 | ADP, MG |
Interfaces
7 interfaces between chains.
- A–F · 648 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 579 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 531 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 492 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 453 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 6CIB · 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 6CIB · PDBe 6CIB · UniProt Q8TZ25
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