MolNFT v1 · #164666 · protein
Structure determination of the transactivation domain of P53 in complex with S100A4 using annexin A2 as a crystallization chaperone
6T58 · Cellular tumor antigen P53,PROTEIN S100-A4,PROTEIN S100-A4…: “Structure determination of the transactivation domain of P53 in complex with S100A4 using annexin A2 as a…”. X-ray diffraction, 1 ligand (CA), 14 pockets (best…
- PDB
- 6T58
- Type
- protein
- Length
- 835 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53,PROTEIN S100-A4,PROTEIN S100-A4, annexin A2
- UniProt
- P04637, P26447, P07355
- Ligands
- CA
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53,PROTEIN S100-A4,PROTEIN S100-A4, annexin A2 | protein | 524 | 67% helix, 1% strand | P04637, P26447, P07355 |
| B | Cellular tumor antigen P53,PROTEIN S100-A4,PROTEIN S100-A4, annexin A2 | protein | 311 | 70% helix, 0% strand | P04637, P26447, P07355 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.75 | 0.88 | 37 | empty |
| 2 | 763 | 0.70 | 0.76 | 58 | CA, GOL |
| 3 | 366 | 0.59 | 0.76 | 36 | empty |
| 4 | 267 | 0.59 | 0.78 | 34 | empty |
| 5 | 304 | 0.56 | 0.76 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 509 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6T58 · Structure determination of the transactivation domain of p53 in complex with S100A4 using… · the same entry in another collection · chain A against A, TM-score 1.00
- P07355 · AlphaFold monomer V2.0 prediction for annexin A2 (P07355) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P26447 · AlphaFold monomer V2.0 prediction for protein S100-A4 (P26447) · a predicted model of the same protein · chain A against A, TM-score 0.17
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 P04637
- Every structure of UniProt P26447
- Every structure of UniProt P07355
- Elsewhere: RCSB PDB 6T58 · PDBe 6T58 · UniProt P04637 · UniProt P26447 · UniProt P07355
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