MolNFT v1 · #79269 · protein

Improved crystal structure of pseudomonas aeruginosa oprd

3SY7 · Porin D: “Improved crystal structure of pseudomonas aeruginosa oprd”. X-ray diffraction, 3 pockets (best druggability 0.57). MolNFT v1 #79269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SY7
Type: protein
Length: 382 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Porin D
EC: 3.4.21.-
UniProt: P32722
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Porin D (EC 3.4.21.-)	protein	382	3% helix, 59% strand	P32722

Ligands and binding sites

C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 8 copies · chains A

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	313	0.57	0.76	48	empty
2	395	0.56	0.75	59	empty
3	236	0.49	0.74	33	empty

Compared structures

3SY7 · Improved crystal structure of Pseudomonas aeruginosa OprD · the same entry in another collection · chain A against A, TM-score 1.00
P32722 · AlphaFold monomer V2.0 prediction for porin D (P32722) · a predicted model of the same protein · chain A 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 P32722
Elsewhere: RCSB PDB 3SY7 · PDBe 3SY7 · UniProt P32722

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