MolNFT v1 · #128598 · protein

Crystal structure of the human 4EHP-GIGYF2 complex

5NVL · Eukaryotic translation initiation factor 4E type 2: “Crystal structure of the human 4EHP-GIGYF2 complex”. X-ray diffraction, 7 pockets (best druggability 0.87). MolNFT v1 #128598 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5NVL
Type: protein
Length: 455 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eukaryotic translation initiation factor 4E type 2; GRB10-interacting gyf protein 2
UniProt: O60573, Q6Y7W6
Pockets: 7 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Eukaryotic translation initiation factor 4E type 2	protein	163	26% helix, 33% strand	O60573
B	GRB10-interacting gyf protein 2	protein	69	46% helix, 3% strand	Q6Y7W6
C	Eukaryotic translation initiation factor 4E type 2	protein	156	27% helix, 35% strand	O60573
D	GRB10-interacting gyf protein 2	protein	67	40% helix, 3% strand	Q6Y7W6

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	477	0.87	0.94	53	empty
2	146	0.42	0.74	19	empty
3	113	0.41	0.76	18	empty
4	79	0.40	0.78	17	empty
5	107	0.38	0.75	17	empty

Interfaces

6 interfaces between chains.

A–B · 2325 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2319 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 491 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 421 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 282 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5NVL · Crystal structure of the human 4EHP-GIGYF2 complex · the same entry in another collection · chain D against D, TM-score 1.00
O60573 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E type 2… · a predicted model of the same protein · chain C against A, TM-score 0.97
Q6Y7W6 · AlphaFold monomer V2.0 prediction for GRB10-interacting gyf protein 2 (Q6Y7W6) · a predicted model of the same protein · chain D against A, TM-score 0.65

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 O60573
Every structure of UniProt Q6Y7W6
Elsewhere: RCSB PDB 5NVL · PDBe 5NVL · UniProt O60573 · UniProt Q6Y7W6

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