MolNFT v1 · #166895 · protein

Crystal structure analysis of zebra fish mdm

6V4E · Protein MDM4: “Crystal structure analysis of zebra fish mdm”. X-ray diffraction, 2 ligands (0EH, NH2), 3 pockets (best druggability 0.67). MolNFT v1 #166895 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6V4E
Type: protein
Length: 206 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein MDM4; Stapled peptide QSQQTF(0EH)NLWRLL(MK8)QN(NH2)
UniProt: Q7ZUW7
Ligands: 0EH, NH2
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein MDM4	protein	90	44% helix, 18% strand	Q7ZUW7
C, D	Stapled peptide QSQQTF(0EH)NLWRLL(MK8)QN(NH2)	protein	13	54% helix, 0% strand	—

Ligands and binding sites

0EH · (2R)-2-amino-2-methylnonanoic acid · ligand · 2 copies · chains A, B, C, D
NH2 · Amino group · ion · 2 copies · chains C, D

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

Pockets

3 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	279	0.67	0.83	41	0EH
2	58	0.35	0.78	15	empty
3	59	0.31	0.75	15	empty

Interfaces

5 interfaces between chains.

A–C · 539 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 528 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 275 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 98 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 96 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

6V4E · Crystal Structure Analysis of Zebra Fish MDM · the same entry in another collection · chain A against A, TM-score 1.00
Q7ZUW7 · AlphaFold monomer V2.0 prediction for protein MDM4 (Q7ZUW7) · a predicted model of the same protein · chain A 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 Q7ZUW7
Elsewhere: RCSB PDB 6V4E · PDBe 6V4E · UniProt Q7ZUW7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.