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Structure of ycao enzyme from methanocaldococcus jannaschii in complex with peptide
Analyse Structure of ycao enzyme from methanocaldococcus jannaschii in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PEU
- Type
- protein
- Length
- 1,580 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein MJ1094; Gly-arg-leu-gly-phe-tyr-gly-tyr-asp-leu-gln-asp
- UniProt
- Q58494
- Ligands
- ATP, MG
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein MJ1094 | protein | 384 | 40% helix, 23% strand | Q58494 |
| B | Uncharacterized protein MJ1094 | protein | 385 | 40% helix, 23% strand | Q58494 |
| C | Uncharacterized protein MJ1094 | protein | 383 | 40% helix, 23% strand | Q58494 |
| D | Uncharacterized protein MJ1094 | protein | 380 | 39% helix, 21% strand | Q58494 |
| M, N, P, Q | Gly-arg-leu-gly-phe-tyr-gly-tyr-asp-leu-gln-asp | protein | 12 | 0% helix, 17% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, M, B, N, C, P, D, Q
- MG · Magnesium ion · metal · 7 copies · chains A, M, B, N, C, P, D, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.85 | 0.96 | 44 | ATP, MG |
| 2 | 308 | 0.84 | 0.95 | 45 | ATP, MG |
| 3 | 229 | 0.84 | 0.97 | 44 | ATP, MG |
| 4 | 239 | 0.83 | 0.96 | 42 | ATP, MG |
| 5 | 890 | 0.81 | 0.83 | 91 | empty |
Interfaces
12 interfaces between chains.
- A–M · 1151 Ų buried · 24 hydrogen bonds · protein-protein
- C–P · 1125 Ų buried · 25 hydrogen bonds · protein-protein
- D–Q · 1112 Ų buried · 24 hydrogen bonds · protein-protein
- B–N · 1108 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 702 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6PEU · Structure of YcaO enzyme from Methanocaldococcus jannaschii in complex with peptide · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q58494 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ1094 (Q58494) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q58494
- Elsewhere: RCSB PDB 6PEU · PDBe 6PEU · UniProt Q58494
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