MolNFT v1 · #11594 · protein

Crystal structure of ERV2P

1JRA · ERV2 protein, mitochondrial: “Crystal structure of ERV2P”. X-ray diffraction, 1 ligand (FAD), 9 pockets (best druggability 0.71). MolNFT v1 #11594 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JRA
Type: protein
Length: 420 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ERV2 protein, mitochondrial
UniProt: Q12284
Ligands: FAD
Pockets: 9 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ERV2 protein, mitochondrial	protein	106	67% helix, 0% strand	Q12284
C	ERV2 protein, mitochondrial	protein	105	67% helix, 0% strand	Q12284
D	ERV2 protein, mitochondrial	protein	103	67% helix, 0% strand	Q12284

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, C

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	293	0.71	0.85	35	FAD
2	164	0.70	0.89	28	FAD
3	85	0.64	0.90	21	empty
4	94	0.64	0.90	19	FAD
5	111	0.64	0.88	22	FAD

Interfaces

5 interfaces between chains.

A–B · 1236 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1101 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 279 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 110 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 50 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

1JRA · Crystal Structure of Erv2p · the same entry in another collection · chain D against D, TM-score 1.00
Q12284 · AlphaFold monomer V2.0 prediction for FAD-linked sulfhydryl oxidase ERV2 (Q12284) · 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 Q12284
Elsewhere: RCSB PDB 1JRA · PDBe 1JRA · UniProt Q12284

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