MolNFT v1 · #63972 · protein

The crystal structure of the complex between evasin-1 and CCL3

3FPT: “The crystal structure of the complex between evasin-1 and CCL3”. X-ray diffraction, 1 ligand (NAG), 2 pockets (best druggability 0.35). MolNFT v1 #63972 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3FPT
Type: protein
Length: 249 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Evasin-1
UniProt: P0C8E7
Ligands: NAG
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Evasin-1	protein	88	9% helix, 44% strand	P0C8E7
B	Evasin-1	protein	79	9% helix, 39% strand	P0C8E7
C	Evasin-1	protein	82	9% helix, 49% strand	P0C8E7

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.35	0.75	18	empty
2	100	0.33	0.72	22	empty

Interfaces

3 interfaces between chains.

A–B · 946 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 763 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 34 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

3FPT · The Crystal Structure of the Complex between Evasin-1 and CCL3 · the same entry in another collection · chain A against A, TM-score 1.00
P0C8E7 · AlphaFold monomer V2.0 prediction for evasin-1 (P0C8E7) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 P0C8E7
Elsewhere: RCSB PDB 3FPT · PDBe 3FPT · UniProt P0C8E7

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