MolNFT v1 · #72652 · protein

Crystal structure of the kinase domain of MPP1/P55

3NEY · 55 kda erythrocyte membrane protein: “Crystal structure of the kinase domain of MPP1/P55”. X-ray diffraction, 2 ligands (UNX, SO4), 16 pockets (best druggability 0.75). MolNFT v1 #72652 on GenesisL1: 3D structure, binding sites and…

PDB: 3NEY
Type: protein
Length: 1,075 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 55 kda erythrocyte membrane protein
UniProt: Q00013
Ligands: UNX, SO4
Pockets: 16 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	55 kda erythrocyte membrane protein	protein	180	39% helix, 24% strand	Q00013
F	55 kda erythrocyte membrane protein	protein	175	40% helix, 24% strand	Q00013

Ligands and binding sites

UNX · Unknown atom or ion · ion · 31 copies · chains A, B, C, D, F, E
SO4 · Sulfate ion · ion · 12 copies · chains A, E, B, C, D, F

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

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	642	0.75	0.81	75	UNX
2	208	0.66	0.85	23	empty
3	507	0.66	0.77	55	SO4, UNX
4	443	0.65	0.78	46	SO4, UNX
5	279	0.63	0.80	44	UNX

Interfaces

13 interfaces between chains.

C–D · 568 Å² buried · 11 hydrogen bonds · protein-protein
F–E · 565 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 547 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 411 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 406 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3NEY · Crystal structure of the kinase domain of MPP1/p55 · the same entry in another collection · chain E against E, TM-score 1.00
Q00013 · AlphaFold monomer V2.0 prediction for 55 kda erythrocyte membrane protein (Q00013) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 Q00013
Elsewhere: RCSB PDB 3NEY · PDBe 3NEY · UniProt Q00013

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