MolNFT v1 · #123403 · protein

Crystal structure of treponema pallidum protein TP0624

5JIR · Oop family ompa-ompf porin: “Crystal structure of treponema pallidum protein TP0624”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.60). MolNFT v1 #123403 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5JIR
Type: protein
Length: 818 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oop family ompa-ompf porin
UniProt: O83632
Ligands: CL
Pockets: 12 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Oop family ompa-ompf porin	protein	405	35% helix, 25% strand	O83632
A	Oop family ompa-ompf porin	protein	413	36% helix, 25% strand	O83632

Ligands and binding sites

CL · Chloride ion · ion · 8 copies · chains B, A
GOL · Glycerol · additive · 4 copies · chains B, A

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

Pockets

12 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	364	0.60	0.77	45	empty
2	105	0.55	0.84	19	GOL
3	107	0.54	0.83	21	empty
4	164	0.54	0.80	32	CL
5	336	0.53	0.74	38	empty

Interfaces

1 interface between chains.

B–A · 1440 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5JIR · Crystal structure of Treponema pallidum protein Tp0624 · the same entry in another collection · chain B against B, 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 O83632
Elsewhere: RCSB PDB 5JIR · PDBe 5JIR · UniProt O83632

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