Research workbench
Structural study of project id PH0250 from pyrococcus horikoshii OT3
Analyse Structural study of project id PH0250 from pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EKD
- Type
- protein
- Length
- 1,219 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH0250
- UniProt
- O57988
- Ligands
- CL
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Hypothetical protein PH0250 | protein | 203 | 37% helix, 26% strand | O57988 |
| F | Hypothetical protein PH0250 | protein | 204 | 37% helix, 26% strand | O57988 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.76 | 0.97 | 24 | empty |
| 2 | 66 | 0.73 | 0.97 | 23 | empty |
| 3 | 110 | 0.60 | 0.86 | 22 | empty |
| 4 | 123 | 0.58 | 0.84 | 22 | empty |
| 5 | 119 | 0.55 | 0.83 | 24 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1096 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1068 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1053 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1053 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1032 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2EKD · Structural study of Project ID PH0250 from Pyrococcus horikoshii OT3 · 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 O57988
- Elsewhere: RCSB PDB 2EKD · PDBe 2EKD · UniProt O57988
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