MolNFT v1 · #141442 · protein
Crystal structure of NDP52 skich region in complex with NAP1
5Z7L · Calcium-binding and coiled-coil domain-containing protein 2: “Crystal structure of NDP52 skich region in complex with NAP1”. X-ray diffraction, 1 pocket (best druggability 0.28). MolNFT v1 #141442 on GenesisL1: 3D structure, binding…
- PDB
- 5Z7L
- Type
- protein
- Length
- 305 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-binding and coiled-coil domain-containing protein 2; 5-azacytidine-induced…
- UniProt
- Q13137, Q9H6S1
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calcium-binding and coiled-coil domain-containing protein 2 | protein | 109 | 11% helix, 36% strand | Q13137 |
| B | Calcium-binding and coiled-coil domain-containing protein 2 | protein | 110 | 8% helix, 38% strand | Q13137 |
| C, D | 5-azacytidine-induced protein 2 | protein | 43 | 91% helix, 0% strand | Q9H6S1 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.28 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1135 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 703 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 655 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 289 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Z7L · Crystal structure of NDP52 SKICH region in complex with NAP1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q13137 · AlphaFold monomer V2.0 prediction for calcium-binding and coiled-coil domain-containing… · a predicted model of the same protein · chain A against A, TM-score 0.94
- Q9H6S1 · AlphaFold monomer V2.0 prediction for 5-azacytidine-induced protein 2 (Q9H6S1) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 Q13137
- Every structure of UniProt Q9H6S1
- Elsewhere: RCSB PDB 5Z7L · PDBe 5Z7L · UniProt Q13137 · UniProt Q9H6S1
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