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Crystal structure of human profilin II

Analyse Crystal structure of human profilin II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1D1J
Type: protein
Length: 549 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Profilin II
UniProt: P35080
Ligands: SO4
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Profilin II	protein	138	29% helix, 31% strand	P35080
B	Profilin II	protein	136	29% helix, 32% strand	P35080
C	Profilin II	protein	137	31% helix, 31% strand	P35080

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains C, D
PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains D

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.79	0.80	82	PG6
2	207	0.54	0.78	31	empty
3	57	0.27	0.74	14	SO4

Interfaces

6 interfaces between chains.

B–D · 701 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 696 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 626 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 283 Å² buried · 1 hydrogen bond · protein-protein
B–C · 144 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1D1J · Crystal structure of human profilin II · the same entry in another collection · chain A against A, TM-score 1.00
P35080 · AlphaFold monomer V2.0 prediction for profilin-2 (P35080) · a predicted model of the same protein · chain C 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 P35080
Elsewhere: RCSB PDB 1D1J · PDBe 1D1J · UniProt P35080

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