Research workbench

Zinc-bound manganese uptake regulator

Analyse Zinc-bound manganese uptake regulator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FD6
Type: protein
Length: 532 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferric uptake regulation protein
UniProt: O07315
Ligands: ZN, SO4
Pockets: 4 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ferric uptake regulation protein	protein	135	40% helix, 26% strand	O07315
B, C	Ferric uptake regulation protein	protein	132	42% helix, 24% strand	O07315
D	Ferric uptake regulation protein	protein	133	42% helix, 24% strand	O07315

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, D
GOL · Glycerol · additive · chains C, D

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

Pockets

4 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	976	0.86	0.87	101	empty
2	232	0.64	0.83	39	empty
3	50	0.34	0.79	15	empty
4	78	0.33	0.75	18	empty

Interfaces

6 interfaces between chains.

A–B · 1556 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1523 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 993 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 686 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 550 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5FD6 · zinc-bound manganese uptake regulator · the same entry in another collection · chain D against D, TM-score 1.00
O07315 · AlphaFold monomer V2.0 prediction for ferric uptake regulation protein (O07315) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 O07315
Elsewhere: RCSB PDB 5FD6 · PDBe 5FD6 · UniProt O07315

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