MolNFT v1 · #156195 · protein

Crystal structure of the human formyl peptide receptor 2 in complex with wkymvm

6LW5 · Soluble cytochrome B562,N-formyl peptide receptor 2: “Crystal structure of the human formyl peptide receptor 2 in complex with wkymvm”. X-ray diffraction, 1 ligand (CLR), 5 pockets (best druggability 0.81). MolNFT v1 #156195 on…

PDB: 6LW5
Type: protein
Length: 433 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble cytochrome B562,N-formyl peptide receptor 2; TRP-lys-tyr-met-val-qxv
UniProt: P0ABE7, P25090
Ligands: CLR
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 75% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Soluble cytochrome B562,N-formyl peptide receptor 2	protein	427	76% helix, 3% strand	P0ABE7, P25090
B	TRP-lys-tyr-met-val-qxv	protein	6	0% helix, 0% strand	—

Ligands and binding sites

CLR · Cholesterol · ligand · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.81	0.98	22	empty
2	262	0.68	0.84	31	empty
3	301	0.62	0.80	37	empty
4	67	0.47	0.83	13	empty
5	56	0.36	0.78	12	empty

Interfaces

1 interface between chains.

A–B · 852 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

6LW5 · Crystal structure of the human formyl peptide receptor 2 in complex with WKYMVm · the same entry in another collection · chain A against A, TM-score 1.00
P25090 · AlphaFold monomer V2.0 prediction for N-formyl peptide receptor 2 (P25090) · a predicted model of the same protein · chain A against A, TM-score 0.67
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.23

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 P0ABE7
Every structure of UniProt P25090
Elsewhere: RCSB PDB 6LW5 · PDBe 6LW5 · UniProt P0ABE7 · UniProt P25090

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