MolNFT v1 · #126003 · protein
Crystal structure of annexin A2 complexed with S100A4
5LPU: “Crystal structure of annexin A2 complexed with S100A4”. X-ray diffraction, 2 ligands (ACE, CA), 9 pockets (best druggability 0.76). MolNFT v1 #126003 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LPU
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Annexin A2; Protein S100-A4
- UniProt
- P07355, P26447
- Ligands
- ACE, CA
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Annexin A2 | protein | 338 | 70% helix, 0% strand | P07355 |
| C | Protein S100-A4 | protein | 89 | 67% helix, 2% strand | P26447 |
| D | Protein S100-A4 | protein | 95 | 65% helix, 2% strand | P26447 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.76 | 0.79 | 101 | GOL |
| 2 | 146 | 0.57 | 0.83 | 24 | empty |
| 3 | 113 | 0.53 | 0.82 | 23 | GOL |
| 4 | 174 | 0.53 | 0.79 | 20 | empty |
| 5 | 84 | 0.50 | 0.83 | 21 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1379 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1134 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 721 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 380 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5LPU · Crystal structure of Annexin A2 complexed with S100A4 · the same entry in another collection · chain D against D, TM-score 1.00
- P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P26447 · AlphaFold monomer V2.0 prediction for protein S100-A4 (P26447) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P07355
- Every structure of UniProt P26447
- Elsewhere: RCSB PDB 5LPU · PDBe 5LPU · UniProt P07355 · UniProt P26447
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