MolNFT v1 · #178194 · protein

Stapled peptide inhibitor in complex with PSD95 gk domain

7F7I · Disks large homolog 4: “Stapled peptide inhibitor in complex with PSD95 gk domain”. X-ray diffraction, 2 ligands (ACE, NH2), 16 pockets (best druggability 0.80). MolNFT v1 #178194 on GenesisL1: 3D structure, binding sites and…

PDB: 7F7I
Type: protein
Length: 1,173 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Disks large homolog 4; ACE-arg-ile-arg-arg-asp-glu-tyr-leu-lyz-ala-ile-gln-NH2
UniProt: P31016
Ligands: ACE, NH2
Pockets: 16 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, F	Disks large homolog 4	protein	182	45% helix, 20% strand	P31016
B	Disks large homolog 4	protein	191	43% helix, 19% strand	P31016
G, H, I, J, K, L	ACE-arg-ile-arg-arg-asp-glu-tyr-leu-lyz-ala-ile-gln-NH2	protein	12	58% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 6 copies · chains A, D, G, B, H, C, I, J, E, K, F, L
NH2 · Amino group · ion · 6 copies · chains G, H, I, J, F, K, E, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1006	0.80	0.82	107	ACE
2	1002	0.78	0.80	77	empty
3	499	0.72	0.81	52	empty
4	70	0.70	0.95	21	ACE
5	299	0.64	0.81	40	empty

Interfaces

19 interfaces between chains.

B–C · 973 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 772 Å² buried · 10 hydrogen bonds · protein-protein
D–J · 698 Å² buried · 12 hydrogen bonds · protein-protein
F–L · 628 Å² buried · 12 hydrogen bonds · protein-protein
B–I · 626 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent, 6 isopeptide, 6 modified, 1 disulfide (covalent ligand, isopeptide, hydroxylation, disulfide).

Compared structures

7F7I · Stapled Peptide Inhibitor in complex with PSD95 GK domain · the same entry in another collection · chain L against L, TM-score 1.00

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 P31016
Elsewhere: RCSB PDB 7F7I · PDBe 7F7I · UniProt P31016

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