MolNFT v1 · #144953 · protein

MEF2B apo protein structure

6C9L · Myocyte-specific enhancer factor 2B: “MEF2B apo protein structure”. X-ray diffraction, 4 pockets (best druggability 0.67). MolNFT v1 #144953 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C9L
Type: protein
Length: 479 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myocyte-specific enhancer factor 2B
UniProt: Q02080
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Myocyte-specific enhancer factor 2B	protein	84	54% helix, 19% strand	Q02080
B	Myocyte-specific enhancer factor 2B	protein	85	56% helix, 19% strand	Q02080
C	Myocyte-specific enhancer factor 2B	protein	85	55% helix, 19% strand	Q02080
E	Myocyte-specific enhancer factor 2B	protein	64	56% helix, 19% strand	Q02080
F	Myocyte-specific enhancer factor 2B	protein	77	58% helix, 16% strand	Q02080

Pockets

4 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	714	0.67	0.75	57	empty
2	108	0.44	0.78	21	empty
3	70	0.36	0.77	17	empty
4	101	0.31	0.72	23	empty

Interfaces

6 interfaces between chains.

C–D · 3013 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 2962 Å² buried · 39 hydrogen bonds · protein-protein
E–F · 2012 Å² buried · 25 hydrogen bonds · protein-protein
D–F · 406 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 129 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6C9L · MEF2B Apo Protein Structure · the same entry in another collection · chain F against F, TM-score 1.00
Q02080 · AlphaFold monomer V2.0 prediction for myocyte-specific enhancer factor 2B (Q02080) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 Q02080
Elsewhere: RCSB PDB 6C9L · PDBe 6C9L · UniProt Q02080

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