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Crystal structure of pmii in complex with pepstatin a to 2.4 a

Analyse Crystal structure of pmii in complex with pepstatin a to 2.4 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1M43
Type: protein
Length: 672 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasmepsin II; Pepstatin
EC: 3.4.23.39
UniProt: P46925
Ligands: IVA
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Plasmepsin II (EC 3.4.23.39)	protein	331	12% helix, 44% strand	P46925
C, D	Pepstatin	protein	5	0% helix, 20% strand	—

Ligands and binding sites

IVA · Isovaleric acid · ligand · 2 copies · chains A, B, C, D

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

Pockets

5 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	1043	0.77	0.79	89	IVA
2	165	0.49	0.77	27	empty
3	113	0.46	0.79	30	empty
4	80	0.36	0.76	16	empty
5	74	0.35	0.76	22	empty

Interfaces

5 interfaces between chains.

A–B · 1205 Å² buried · 1 hydrogen bond · protein-protein
A–C · 596 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 589 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 53 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 42 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 2 covalent, 2 disulfide (nonstandard, covalent ligand, disulfide).

Compared structures

1M43 · Crystal structure of PMII in complex with pepstatin a to 2.4 A · the same entry in another collection · chain A against A, TM-score 1.00
P46925 · AlphaFold monomer V2.0 prediction for plasmepsin-2 (P46925) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P46925
Elsewhere: RCSB PDB 1M43 · PDBe 1M43 · UniProt P46925

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