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Structure of porin omp-PST1 from P. stuartii; the crystallographic symmetry generates a dimer of trimers.

Analyse Structure of porin omp-PST1 from P. stuartii; the crystallographic symmetry… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4D64
Type: protein
Length: 1,056 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Porin 1
UniProt: E3U904
Ligands: CA
Pockets: 12 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Porin 1	protein	352	7% helix, 59% strand	E3U904

Ligands and binding sites

CA · Calcium ion · metal · chains B, C

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	586	0.86	0.91	41	CA
2	895	0.74	0.78	67	empty
3	1164	0.72	0.76	69	empty
4	1200	0.72	0.76	81	empty
5	249	0.50	0.74	33	empty

Interfaces

3 interfaces between chains.

A–C · 1754 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1721 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 1704 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

4D64 · Structure of porin Omp-Pst1 from P. stuartii; the crystallographic symmetry generates a… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt E3U904
Elsewhere: RCSB PDB 4D64 · PDBe 4D64 · UniProt E3U904

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