MolNFT v1 · #78999 · protein
Crystal structure of human ptip BRCT5/6-gamma H2AX complex
3SQD · Pax-interacting protein 1: “Crystal structure of human ptip BRCT5/6-gamma H2AX complex”. X-ray diffraction, 3 pockets (best druggability 0.42). MolNFT v1 #78999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SQD
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pax-interacting protein 1; Histone H2A.X
- UniProt
- Q6ZW49, P16104
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pax-interacting protein 1 | protein | 211 | 45% helix, 14% strand | Q6ZW49 |
| B | Pax-interacting protein 1 | protein | 205 | 44% helix, 13% strand | Q6ZW49 |
| C | Histone H2A.X | protein | 10 | 0% helix, 0% strand | P16104 |
| D | Histone H2A.X | protein | 4 | 0% helix, 0% strand | P16104 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.42 | 0.77 | 15 | empty |
| 2 | 118 | 0.38 | 0.74 | 21 | empty |
| 3 | 64 | 0.37 | 0.78 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 531 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 355 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3SQD · Crystal structure of human PTIP BRCT5/6-gamma H2AX complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q6ZW49 · AlphaFold monomer V2.0 prediction for pax-interacting protein 1 (Q6ZW49) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P16104 · AlphaFold monomer V2.0 prediction for histone H2AX (P16104) · a predicted model of the same protein · chain D against A, TM-score 0.86
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 Q6ZW49
- Every structure of UniProt P16104
- Elsewhere: RCSB PDB 3SQD · PDBe 3SQD · UniProt Q6ZW49 · UniProt P16104
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