Research workbench
Structural genomics, ybgi protein, unknown function
Analyse Structural genomics, ybgi protein, unknown function in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NMP
- Type
- protein
- Length
- 1,482 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein ybgi
- UniProt
- P75743
- Ligands
- MG
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Hypothetical protein ybgi | protein | 247 | 38% helix, 25% strand | P75743 |
Ligands and binding sites
- MG · Magnesium ion · metal · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.75 | 0.78 | 94 | MG |
| 2 | 450 | 0.72 | 0.82 | 62 | empty |
| 3 | 530 | 0.68 | 0.78 | 48 | MG |
| 4 | 514 | 0.67 | 0.78 | 54 | MG |
| 5 | 546 | 0.67 | 0.78 | 52 | MG |
Interfaces
10 interfaces between chains.
- A–B · 1218 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1215 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1207 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 312 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 154 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1NMP · Structural genomics, ybgI protein, unknown function · 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 P75743
- Elsewhere: RCSB PDB 1NMP · PDBe 1NMP · UniProt P75743
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