MolNFT v1 · #156496 · protein

Crystal structure of SMAD2 in complex with cbp

6M64 · Mothers against decapentaplegic homolog 2: “Crystal structure of SMAD2 in complex with cbp”. X-ray diffraction, 11 pockets (best druggability 0.84). MolNFT v1 #156496 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6M64
Type: protein
Length: 656 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mothers against decapentaplegic homolog 2; Cbp
UniProt: Q15796
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mothers against decapentaplegic homolog 2	protein	203	28% helix, 28% strand	Q15796
B	Cbp	protein	19	79% helix, 0% strand	—
C	Mothers against decapentaplegic homolog 2	protein	194	30% helix, 29% strand	Q15796
D	Cbp	protein	20	80% helix, 0% strand	—
E	Mothers against decapentaplegic homolog 2	protein	193	30% helix, 30% strand	Q15796
F	Cbp	protein	27	63% helix, 0% strand	—

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.84	0.85	104	empty
2	265	0.63	0.81	40	empty
3	234	0.63	0.82	36	empty
4	255	0.59	0.79	38	empty
5	66	0.43	0.82	23	empty

Interfaces

6 interfaces between chains.

A–E · 1486 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 1043 Å² buried · 23 hydrogen bonds · protein-protein
C–E · 973 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 719 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 646 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6M64 · Crystal structure of SMAD2 in complex with CBP · the same entry in another collection · chain F against F, TM-score 1.00
Q15796 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 2 (Q15796) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q15796
Elsewhere: RCSB PDB 6M64 · PDBe 6M64 · UniProt Q15796

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