MolNFT v1 · #118806 · protein

Manganese uptake regulator

5FD5 · Ferric uptake regulation protein: “Manganese uptake regulator”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.85). MolNFT v1 #118806 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FD5
Type: protein
Length: 673 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ferric uptake regulation protein
UniProt: O07315
Ligands: SO4
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ferric uptake regulation protein	protein	137	41% helix, 25% strand	O07315
B	Ferric uptake regulation protein	protein	136	41% helix, 18% strand	O07315
C	Ferric uptake regulation protein	protein	135	41% helix, 25% strand	O07315
D	Ferric uptake regulation protein	protein	133	42% helix, 26% strand	O07315
E	Ferric uptake regulation protein	protein	132	43% helix, 26% strand	O07315

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains B, C, D, A, E
EDO · 1,2-ethanediol · additive · 3 copies · chains C, D, A, E

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

Pockets

9 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	450	0.85	0.93	67	SO4
2	919	0.84	0.86	134	EDO
3	426	0.71	0.82	72	SO4, EDO
4	328	0.61	0.78	45	empty
5	74	0.44	0.81	16	empty

Interfaces

9 interfaces between chains.

C–D · 1773 Å² buried · 21 hydrogen bonds · protein-protein
A–E · 1769 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1687 Å² buried · 23 hydrogen bonds · protein-protein
C–E · 1640 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 919 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5FD5 · manganese uptake regulator · the same entry in another collection · chain E against E, TM-score 1.00
O07315 · AlphaFold monomer V2.0 prediction for ferric uptake regulation protein (O07315) · a predicted model of the same protein · chain A against A, TM-score 0.67

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 5FD5 · PDBe 5FD5 · UniProt O07315

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