Research workbench
Crystal structure of genomics APC5600
Analyse Crystal structure of genomics APC5600 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YNB
- Type
- protein
- Length
- 501 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein AF1432
- UniProt
- O28840
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hypothetical protein AF1432 | protein | 167 | 65% helix, 1% strand | O28840 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.70 | 0.92 | 28 | empty |
| 2 | 301 | 0.66 | 0.82 | 48 | empty |
| 3 | 145 | 0.66 | 0.87 | 35 | empty |
| 4 | 302 | 0.56 | 0.76 | 33 | empty |
| 5 | 239 | 0.53 | 0.77 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2677 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1100 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 414 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1YNB · crystal structure of genomics APC5600 · the same entry in another collection · chain A against A, TM-score 1.00
- 1YOY · Predicted coding region AF1432 from Archaeoglobus Fulgidus · a predicted model of the same protein · chain C against A, TM-score 0.87
- 1YOY · Predicted coding region AF1432 from archaeoglobus fulgidus · a predicted model of the same protein · chain A against A, TM-score 0.87
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 O28840
- Elsewhere: RCSB PDB 1YNB · PDBe 1YNB · UniProt O28840
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