MolNFT v1 · #106755 · protein

1.80A resolution structure of bfrb (C89S, K96C) crystal form 2 from pseudomonas aeruginosa

4TOG · Bacterioferritin: “1.80A resolution structure of bfrb (C89S, K96C) crystal form 2 from pseudomonas aeruginosa”. X-ray diffraction, 4 ligands (HEM, NA, K), 7 pockets (best druggability 0.73). MolNFT v1 #106755 on GenesisL1: 3D…

PDB: 4TOG
Type: protein
Length: 625 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacterioferritin
EC: 1.16.3.1
UniProt: Q9HY79
Ligands: HEM, NA, K, SO4
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Bacterioferritin (EC 1.16.3.1)	protein	156	78% helix, 0% strand	Q9HY79
C	Bacterioferritin (EC 1.16.3.1)	protein	157	78% helix, 0% strand	Q9HY79

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C, D
NA · Sodium ion · metal · 4 copies · chains A, B, C, D
K · Potassium ion · metal · chains B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains B, A, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, D, B, C

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

Pockets

7 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	214	0.73	0.88	33	HEM
2	296	0.57	0.77	34	MPD
3	170	0.43	0.75	16	empty
4	110	0.42	0.77	17	empty
5	81	0.41	0.78	16	MPD

Interfaces

5 interfaces between chains.

A–B · 916 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 516 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 514 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 511 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 52 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4TOG · 1.80A resolution structure of BfrB (C89S, K96C) crystal form 2 from Pseudomonas aeruginosa · the same entry in another collection · chain B against B, 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 Q9HY79
Elsewhere: RCSB PDB 4TOG · PDBe 4TOG · UniProt Q9HY79

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