Research workbench
Structure of caprine serum albumin in P1 space group
Analyse Structure of caprine serum albumin in P1 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OTB
- Type
- protein
- Length
- 2,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Albumin
- UniProt
- B3VHM9
- Ligands
- PRO
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Albumin | protein | 581 | 74% helix, 0% strand | B3VHM9 |
Ligands and binding sites
- PRO · Proline · ligand · 11 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.86 | 0.88 | 93 | PRO |
| 2 | 696 | 0.84 | 0.87 | 69 | empty |
| 3 | 498 | 0.83 | 0.90 | 57 | PRO |
| 4 | 602 | 0.82 | 0.87 | 71 | empty |
| 5 | 594 | 0.81 | 0.86 | 78 | PEG |
Interfaces
4 interfaces between chains.
- A–B · 1238 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1078 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 561 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 246 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 68 disulfide (disulfide).
Compared structures
- 5OTB · Structure of caprine serum albumin in P1 space group · 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 B3VHM9
- Elsewhere: RCSB PDB 5OTB · PDBe 5OTB · UniProt B3VHM9
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