MolNFT v1 · #80061 · protein

Crystal structure of holo fepb

3TLK · Ferrienterobactin-binding periplasmic protein: “Crystal structure of holo fepb”. X-ray diffraction, 2 ligands (EB4, FE), 7 pockets (best druggability 0.78). MolNFT v1 #80061 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3TLK
Type: protein
Length: 882 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferrienterobactin-binding periplasmic protein
UniProt: P0AEL6
Ligands: EB4, FE
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ferrienterobactin-binding periplasmic protein	protein	296	39% helix, 22% strand	P0AEL6
B	Ferrienterobactin-binding periplasmic protein	protein	291	39% helix, 22% strand	P0AEL6
C	Ferrienterobactin-binding periplasmic protein	protein	295	39% helix, 21% strand	P0AEL6

Ligands and binding sites

EB4 · N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) · ligand · 4 copies · chains A, C, B
FE · Fe (III) ion · metal · 4 copies · chains A, B, C
DIO · 1,4-diethylene dioxide · additive · 3 copies · chains A, C, B

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

Pockets

7 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	763	0.78	0.82	71	FE, EB4, DIO
2	548	0.78	0.85	65	FE, EB4, DIO
3	499	0.78	0.85	58	FE, EB4, DIO
4	192	0.56	0.80	34	empty
5	52	0.37	0.80	20	empty

Interfaces

3 interfaces between chains.

B–C · 765 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 742 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 677 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3TLK · Crystal structure of holo FepB · the same entry in another collection · chain A against A, TM-score 1.00
P0AEL6 · AlphaFold monomer V2.0 prediction for ferrienterobactin-binding periplasmic protein… · a predicted model of the same protein · chain B 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 P0AEL6
Elsewhere: RCSB PDB 3TLK · PDBe 3TLK · UniProt P0AEL6

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