MolNFT v1 · #170079 · protein

Enah EVH1 in complex with ac-[2-cl-F]-ppppteddl-NH2

6XVT · Protein enabled homolog: “Enah EVH1 in complex with ac-[2-cl-F]-ppppteddl-NH2”. X-ray diffraction, 4 ligands (2L5, NME, NO3), 1 pocket (best druggability 0.62). MolNFT v1 #170079 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6XVT
Type: protein
Length: 229 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein enabled homolog; Acy-SC1-SC2-SC3-SC4-SC5-nme
UniProt: Q8N8S7
Ligands: 2L5, NME, NO3, SO4
Pockets: 1 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein enabled homolog	protein	112	18% helix, 49% strand	Q8N8S7
B	Protein enabled homolog	protein	109	18% helix, 49% strand	Q8N8S7
G, H	Acy-SC1-SC2-SC3-SC4-SC5-nme	protein	4	0% helix, 0% strand	—

Ligands and binding sites

2L5 · 2-chloro-L-phenylalanine · ligand · 2 copies · chains A, B, G, H
NME · Methylamine · ligand · 2 copies · chains G, H
NO3 · Nitrate ion · ion · 5 copies · chains A, B
SO4 · Sulfate ion · ion · chains A
ACY · Acetic acid · additive · 2 copies · chains A, B, G, H

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	256	0.62	0.81	25	ACY, 2L5

Interfaces

5 interfaces between chains.

A–B · 601 Å² buried · 15 hydrogen bonds · protein-protein
B–H · 240 Å² buried · 3 hydrogen bonds · protein-protein
A–G · 237 Å² buried · 3 hydrogen bonds · protein-protein
B–G · 15 Å² buried · 0 hydrogen bonds · protein-protein
A–H · 15 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

6XVT · ENAH EVH1 in complex with Ac-[2-Cl-F]-PPPPTEDDL-NH2 · the same entry in another collection · chain B against B, TM-score 1.00
Q8N8S7 · AlphaFold monomer V2.0 prediction for protein enabled homolog (Q8N8S7) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q8N8S7
Elsewhere: RCSB PDB 6XVT · PDBe 6XVT · UniProt Q8N8S7

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