MolNFT v1 · #34805 · protein

Acanthamoeba myosin I SH3 domain bound to ACAN125

2DRM · Acanthamoeba myosin ib: “Acanthamoeba myosin I SH3 domain bound to ACAN125”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.55). MolNFT v1 #34805 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2DRM
Type: protein
Length: 267 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acanthamoeba myosin ib; 18-mer peptide from ACAN125
UniProt: P19706
Ligands: SO4
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Acanthamoeba myosin ib	protein	58	5% helix, 50% strand	P19706
E	18-mer peptide from ACAN125	protein	18	0% helix, 0% strand	—
G	18-mer peptide from ACAN125	protein	17	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, E, C, B, G, D
GOL · Glycerol · additive · 4 copies · chains B, E, C, G, D, A

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

Pockets

2 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	196	0.55	0.79	36	GOL
2	102	0.36	0.75	24	SO4

Interfaces

9 interfaces between chains.

A–E · 720 Å² buried · 15 hydrogen bonds · protein-protein
C–G · 714 Å² buried · 15 hydrogen bonds · protein-protein
B–E · 394 Å² buried · 7 hydrogen bonds · protein-protein
D–G · 394 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 260 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2DRM · Acanthamoeba myosin I SH3 domain bound to Acan125 · the same entry in another collection · chain D against D, TM-score 1.00
P19706 · AlphaFold monomer V2.0 prediction for myosin heavy chain ib (P19706) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 P19706
Elsewhere: RCSB PDB 2DRM · PDBe 2DRM · UniProt P19706

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