MolNFT v1 · #141432 · protein

Crystal structure of NDP52 skich region

5Z7A · Calcium-binding and coiled-coil domain-containing protein 2: “Crystal structure of NDP52 skich region”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.55). MolNFT v1 #141432 on GenesisL1: 3D structure, binding…

PDB: 5Z7A
Type: protein
Length: 209 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calcium-binding and coiled-coil domain-containing protein 2
UniProt: Q13137
Ligands: SO4
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Calcium-binding and coiled-coil domain-containing protein 2	protein	105	6% helix, 39% strand	Q13137
B	Calcium-binding and coiled-coil domain-containing protein 2	protein	104	3% helix, 38% strand	Q13137

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B
DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A, B
GOL · Glycerol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	137	0.55	0.82	22	DTT, GOL
2	79	0.45	0.81	16	empty
3	81	0.41	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 696 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5Z7A · Crystal structure of NDP52 SKICH region · the same entry in another collection · chain A against A, 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 0.96

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
Elsewhere: RCSB PDB 5Z7A · PDBe 5Z7A · UniProt Q13137

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