MolNFT v1 · #174896 · protein

E30 F-particle in complex with CD55

7C9W · VP1: “E30 F-particle in complex with CD55”. Electron microscopy, 2 ligands (SPH, MYR), 13 pockets (best druggability 0.79). MolNFT v1 #174896 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7C9W
Type: protein
Length: 1,014 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3; VP4; Complement decay-accelerating factor
UniProt: Q33C85, P08174
Ligands: SPH, MYR
Pockets: 13 · best druggability 0.79

Structure

electron microscopy · 5 distinct chains · 6% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	276	7% helix, 26% strand	—
B	VP2	protein	251	6% helix, 36% strand	—
C	VP3	protein	238	8% helix, 28% strand	—
D	VP4	protein	57	7% helix, 16% strand	Q33C85
E	Complement decay-accelerating factor	protein	192	0% helix, 34% strand	P08174

Ligands and binding sites

SPH · Sphingosine · ligand · chains A
MYR · Myristic acid · ligand · chains D

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

Pockets

13 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	551	0.79	0.85	73	SPH
2	547	0.70	0.79	47	empty
3	250	0.51	0.75	37	empty
4	119	0.49	0.80	29	empty
5	80	0.46	0.82	25	empty

Interfaces

8 interfaces between chains.

A–C · 4376 Å² buried · 59 hydrogen bonds · protein-protein
A–B · 2107 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1663 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 1307 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 944 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 lipid (disulfide, myristoylation).

Compared structures

7C9W · E30 F-particle in complex with CD55 · the same entry in another collection · chain A against A, TM-score 1.00
P08174 · AlphaFold monomer V2.0 prediction for complement decay-accelerating factor (P08174) · a predicted model of the same protein · chain E against A, TM-score 0.87

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 Q33C85
Every structure of UniProt P08174
Elsewhere: RCSB PDB 7C9W · PDBe 7C9W · UniProt Q33C85 · UniProt P08174

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