MolNFT v1 · #50863 · protein

SEM5 SH3 domain complexed with peptoid inhibitor

2SEM · Protein (sex muscle abnormal protein 5): “SEM5 SH3 domain complexed with peptoid inhibitor”. X-ray diffraction, 1 ligand (ACE), 1 pocket (best druggability 0.31). MolNFT v1 #50863 on GenesisL1: 3D structure, binding sites and…

PDB: 2SEM
Type: protein
Length: 132 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (sex muscle abnormal protein 5); Protein (SH3 peptoid inhibitor)
UniProt: P29355
Ligands: ACE
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein (sex muscle abnormal protein 5)	protein	58	5% helix, 48% strand	P29355
B	Protein (sex muscle abnormal protein 5)	protein	59	5% helix, 49% strand	P29355
C	Protein (SH3 peptoid inhibitor)	protein	7	0% helix, 0% strand	—
D	Protein (SH3 peptoid inhibitor)	protein	8	0% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	64	0.31	0.75	13	empty

Interfaces

3 interfaces between chains.

B–D · 441 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 421 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 264 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified, 1 disulfide (covalent ligand, nonstandard, disulfide).

Compared structures

2SEM · SEM5 SH3 domain complexed with peptoid inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P29355 · AlphaFold monomer V2.0 prediction for sex muscle abnormal protein 5 (P29355) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P29355
Elsewhere: RCSB PDB 2SEM · PDBe 2SEM · UniProt P29355

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