MolNFT v1 · #166898 · protein

Crystal structure analysis of zebra fish mdmx

6V4H · Protein MDM4: “Crystal structure analysis of zebra fish mdmx”. X-ray diffraction, 2 ligands (0EH, NH2), 2 pockets (best druggability 0.67). MolNFT v1 #166898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6V4H
Type: protein
Length: 205 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein MDM4; Stapled peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)
UniProt: Q7ZUW7
Ligands: 0EH, NH2
Pockets: 2 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein MDM4	protein	90	44% helix, 18% strand	Q7ZUW7
B	Stapled peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)	protein	13	54% helix, 0% strand	—
D	Stapled peptide LSQETF(0EH)DLWKLL(MK8)EN(NH2)	protein	12	58% 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 B, D

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

Pockets

2 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	307	0.67	0.82	47	0EH
2	56	0.29	0.74	14	empty

Interfaces

5 interfaces between chains.

A–B · 542 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 532 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 304 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 101 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 94 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6V4H · Crystal Structure Analysis of Zebra Fish MDMX · 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 6V4H · PDBe 6V4H · UniProt Q7ZUW7

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