MolNFT v1 · #170082 · protein

Human myelin protein P2 mutant R88Q

6XVY · Myelin P2 protein: “Human myelin protein P2 mutant R88Q”. X-ray diffraction, 2 ligands (PLM, CL), 8 pockets (best druggability 0.84). MolNFT v1 #170082 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XVY
Type: protein
Length: 532 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myelin P2 protein
UniProt: P02689
Ligands: PLM, CL
Pockets: 8 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, C, D, E	Myelin P2 protein	protein	133	14% helix, 57% strand	P02689

Ligands and binding sites

PLM · Palmitic acid · ligand · 4 copies · chains B, C, D, E
CL · Chloride ion · ion · 4 copies · chains B, C, D, E
CIT · Citric acid · additive · 2 copies · chains C, E, D

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

Pockets

8 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	295	0.84	0.95	36	PLM
2	300	0.82	0.93	37	PLM
3	325	0.82	0.92	35	PLM
4	322	0.82	0.92	36	PLM
5	733	0.72	0.78	65	empty

Interfaces

5 interfaces between chains.

B–C · 512 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 509 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 342 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 225 Å² buried · 1 hydrogen bond · protein-protein
C–D · 61 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6XVY · Human myelin protein P2 mutant R88Q · the same entry in another collection · chain B against B, TM-score 1.00
P02689 · AlphaFold monomer V2.0 prediction for myelin P2 protein (P02689) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P02689
Elsewhere: RCSB PDB 6XVY · PDBe 6XVY · UniProt P02689

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