MolNFT v1 · #141955 · protein

Crystal structure of human SMAD2-MAN1 complex

5ZOJ · Mothers against decapentaplegic homolog 2: “Crystal structure of human SMAD2-MAN1 complex”. X-ray diffraction, 7 pockets (best druggability 0.84). MolNFT v1 #141955 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZOJ
Type: protein
Length: 801 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mothers against decapentaplegic homolog 2; Inner nuclear membrane protein MAN1
UniProt: Q15796, Q9Y2U8
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 28% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mothers against decapentaplegic homolog 2	protein	187	29% helix, 30% strand	Q15796
B	Mothers against decapentaplegic homolog 2	protein	185	28% helix, 31% strand	Q15796
C	Mothers against decapentaplegic homolog 2	protein	186	29% helix, 31% strand	Q15796
D	Inner nuclear membrane protein MAN1	protein	127	29% helix, 24% strand	Q9Y2U8
E	Inner nuclear membrane protein MAN1	protein	116	22% helix, 26% strand	Q9Y2U8

Pockets

7 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	1064	0.84	0.85	96	empty
2	292	0.62	0.80	36	empty
3	343	0.61	0.78	32	empty
4	231	0.58	0.79	30	empty
5	166	0.48	0.77	27	empty

Interfaces

5 interfaces between chains.

A–B · 833 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 816 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 790 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 621 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 615 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5ZOJ · Crystal structure of human SMAD2-MAN1 complex · the same entry in another collection · chain E against E, 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 A against A, TM-score 0.99
Q9Y2U8 · AlphaFold monomer V2.0 prediction for inner nuclear membrane protein MAN1 (Q9Y2U8) · a predicted model of the same protein · chain D against A, TM-score 0.98

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
Every structure of UniProt Q9Y2U8
Elsewhere: RCSB PDB 5ZOJ · PDBe 5ZOJ · UniProt Q15796 · UniProt Q9Y2U8

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