MolNFT v1 · #93946 · protein

Crystal structure of an acylphosphatase protein cage

4HI2: “Crystal structure of an acylphosphatase protein cage”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.76). MolNFT v1 #93946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4HI2
Type: protein
Length: 1,058 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acylphosphatase
EC: 3.6.1.7
UniProt: A5F8G9
Ligands: SO4
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E, F, G, H, I, J, L	Acylphosphatase (EC 3.6.1.7)	protein	88	25% helix, 36% strand	A5F8G9
B, K	Acylphosphatase (EC 3.6.1.7)	protein	89	27% helix, 38% strand	A5F8G9

Ligands and binding sites

SO4 · Sulfate ion · ion · 43 copies · chains A, B, K, F, I, C, J, D, H, E, L, G

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	821	0.76	0.80	105	SO4
2	804	0.74	0.79	103	SO4
3	481	0.74	0.83	60	SO4
4	489	0.73	0.82	60	SO4
5	677	0.72	0.79	57	SO4

Interfaces

30 interfaces between chains.

E–L · 406 Å² buried · 6 hydrogen bonds · protein-protein
C–H · 396 Å² buried · 9 hydrogen bonds · protein-protein
B–I · 383 Å² buried · 6 hydrogen bonds · protein-protein
F–K · 379 Å² buried · 8 hydrogen bonds · protein-protein
A–F · 377 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4HI2 · Crystal structure of an Acylphosphatase protein cage · the same entry in another collection · chain L against L, TM-score 1.00

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 A5F8G9
Elsewhere: RCSB PDB 4HI2 · PDBe 4HI2 · UniProt A5F8G9

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