MolNFT v1 · #27179 · protein

Oxo ZIRCONIUM(IV) cluster in the ferric binding protein (fbp)

1XC1 · Periplasmic iron-binding protein: “Oxo ZIRCONIUM(IV) cluster in the ferric binding protein (fbp)”. X-ray diffraction, 1 ligand (ZRC), 20 pockets (best druggability 0.73). MolNFT v1 #27179 on GenesisL1: 3D structure, binding sites…

PDB: 1XC1
Type: protein
Length: 2,781 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic iron-binding protein
Ligands: ZRC
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I	Periplasmic iron-binding protein	protein	309	45% helix, 17% strand	—

Ligands and binding sites

ZRC · Oxo zirconium(iv) cluster · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1044	0.73	0.77	102	ZRC
2	947	0.71	0.76	109	ZRC
3	513	0.68	0.79	79	ZRC
4	435	0.67	0.79	59	ZRC
5	359	0.66	0.80	62	empty

Interfaces

12 interfaces between chains.

A–I · 344 Å² buried · 5 hydrogen bonds · protein-protein
F–I · 342 Å² buried · 3 hydrogen bonds · protein-protein
B–G · 320 Å² buried · 1 hydrogen bond · protein-protein
A–H · 302 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 244 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1XC1 · Oxo Zirconium(IV) Cluster in the Ferric Binding Protein (FBP) · 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
Elsewhere: RCSB PDB 1XC1 · PDBe 1XC1

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