MolNFT v1 · #129195 · protein

Periplasmic binding protein ceue complexed with a synthetic catalyst

5OD5 · Enterochelin ABC transporter substrate-binding protein: “Periplasmic binding protein ceue complexed with a synthetic catalyst”. X-ray diffraction, 7 ligands (95B, 9RT, RIR), 8 pockets (best druggability 0.66). MolNFT v1 #129195 on…

PDB: 5OD5
Type: protein
Length: 864 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Enterochelin ABC transporter substrate-binding protein
UniProt: A0A1E7P069
Ligands: 95B, 9RT, RIR, 7PG, IR, FE, PO4
Pockets: 8 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Enterochelin ABC transporter substrate-binding protein	protein	288	41% helix, 21% strand	A0A1E7P069

Ligands and binding sites

95B · Azotochelin · ligand · 2 copies · chains A, C
9RT · 4-(aminomethyl)-~{N}-(pyridin-2-ylmethyl)benzenesulfonamide · ligand · 2 copies · chains A, C
RIR · [(1,2,3,4,5-Eta)-1,2,3,4,5-Pentamethylcyclopentadienyl]iridium(III) · ligand · 2 copies · chains A, C
7PG · 2,5,8,11,14,17,20,23-octaoxapentacosan-25-ol · ligand · chains A, B
IR · Iridium ion · metal · 6 copies · chains A, B, C
FE · Fe (III) ion · metal · 3 copies · chains A, B, C
PO4 · Phosphate ion · ion · 3 copies · chains A, C

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

Pockets

8 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	313	0.66	0.81	42	FE
2	385	0.65	0.79	33	empty
3	427	0.63	0.77	42	empty
4	181	0.61	0.83	28	FE
5	384	0.60	0.76	45	empty

Interfaces

3 interfaces between chains.

A–B · 557 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 549 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 287 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5OD5 · Periplasmic binding protein CeuE complexed with a synthetic catalyst · the same entry in another collection · chain A against A, 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 A0A1E7P069
Elsewhere: RCSB PDB 5OD5 · PDBe 5OD5 · UniProt A0A1E7P069

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