MolNFT v1 · #51636 · protein
Structure of human serum albumin with S-naproxen and the ga module
2VDB: “Structure of human serum albumin with S-naproxen and the ga module”. X-ray diffraction, 2 ligands (DKA, NPS), 9 pockets (best druggability 0.87). MolNFT v1 #51636 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VDB
- Type
- protein
- Length
- 629 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin; Peptostreptococcal albumin-binding protein
- UniProt
- P02768, Q51911
- Ligands
- DKA, NPS
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serum albumin | protein | 574 | 69% helix, 0% strand | P02768 |
| B | Peptostreptococcal albumin-binding protein | protein | 55 | 76% helix, 0% strand | Q51911 |
Ligands and binding sites
- DKA · Decanoic acid · ligand · 6 copies · chains A, B
- NPS · (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.87 | 0.91 | 77 | DKA |
| 2 | 612 | 0.86 | 0.91 | 66 | DKA |
| 3 | 224 | 0.72 | 0.87 | 25 | DKA, NPS |
| 4 | 150 | 0.72 | 0.90 | 25 | empty |
| 5 | 305 | 0.61 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 965 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 2VDB · Structure of human serum albumin with S-naproxen and the GA module · the same entry in another collection · chain A against A, TM-score 1.00
- Q51911 · AlphaFold monomer V2.0 prediction for peptostreptococcal albumin- binding protein (Q51911) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P02768 · AlphaFold monomer V2.0 prediction for albumin (P02768) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P02768
- Every structure of UniProt Q51911
- Elsewhere: RCSB PDB 2VDB · PDBe 2VDB · UniProt P02768 · UniProt Q51911
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