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Crystal structure of a ternary MEF2 CHIMERA/NKX2-5/MYOCARDIN enhancer DNA complex

Analyse Crystal structure of a ternary MEF2 CHIMERA/NKX2-5/MYOCARDIN enhancer DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WC2
Type: protein + DNA
Length: 830 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MEF2 CHIMERA,MYOCYTE-specific enhancer factor 2B,MYOCYTE- specific enhancer factor 2A…
UniProt: Q02078, Q02080, P52952
Pockets: 15 · best druggability 0.76

Structure

x-ray diffraction · 10 distinct chains · 56% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	MEF2 CHIMERA,MYOCYTE-specific enhancer factor 2B,MYOCYTE- specific enhancer factor 2A	protein	91	51% helix, 16% strand	Q02078, Q02080
B	MEF2 CHIMERA,MYOCYTE-specific enhancer factor 2B,MYOCYTE- specific enhancer factor 2A	protein	88	52% helix, 16% strand	Q02078, Q02080
C	MEF2 CHIMERA,MYOCYTE-specific enhancer factor 2B,MYOCYTE- specific enhancer factor 2A	protein	89	49% helix, 17% strand	Q02078, Q02080
D	MEF2 CHIMERA,MYOCYTE-specific enhancer factor 2B,MYOCYTE- specific enhancer factor 2A	protein	93	48% helix, 16% strand	Q02078, Q02080
E, G, K	Myocardin enhancer DNA	dna	21	—	—
F, H, L	Myocardin enhancer DNA	dna	21	—	—
J	MEF2 CHIMERA,MYOCYTE-specific enhancer factor 2B,MYOCYTE- specific enhancer factor 2A	protein	92	49% helix, 16% strand	Q02078, Q02080
M	Homeobox protein nkx-2.5	protein	54	72% helix, 0% strand	P52952
N	Homeobox protein nkx-2.5	protein	53	74% helix, 0% strand	P52952
O	Homeobox protein nkx-2.5	protein	53	74% helix, 0% strand	P52952

Pockets

15 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	872	0.76	0.80	75	empty
2	901	0.75	0.79	57	empty
3	802	0.73	0.78	73	empty
4	385	0.67	0.80	32	empty
5	654	0.64	0.75	63	empty

Interfaces

35 interfaces between chains.

I–J · 3238 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 3181 Å² buried · 40 hydrogen bonds · protein-protein
C–D · 3094 Å² buried · 42 hydrogen bonds · protein-protein
E–F · 937 Å² buried · 72 hydrogen bonds · nucleic-nucleic
G–H · 924 Å² buried · 69 hydrogen bonds · nucleic-nucleic

Compared structures

6WC2 · Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex · the same entry in another collection · chain K against K, 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 Q02078
Every structure of UniProt Q02080
Every structure of UniProt P52952
Elsewhere: RCSB PDB 6WC2 · PDBe 6WC2 · UniProt Q02078 · UniProt Q02080 · UniProt P52952

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