MolNFT v1 · #116593 · protein

Structure of an engineered bacterial microcompartment shell protein binding a [4FE-4S] cluster

5DII · Microcompartments protein: “Structure of an engineered bacterial microcompartment shell protein binding a [4FE-4S] cluster”. X-ray diffraction, 1 ligand (SF4), 16 pockets (best druggability 0.47). MolNFT v1 #116593 on GenesisL1: 3D…

PDB: 5DII
Type: protein
Length: 1,180 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microcompartments protein
UniProt: D0LHE3
Ligands: SF4
Pockets: 16 · best druggability 0.47

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Microcompartments protein	protein	194	35% helix, 30% strand	D0LHE3
B	Microcompartments protein	protein	196	33% helix, 30% strand	D0LHE3
C	Microcompartments protein	protein	199	36% helix, 30% strand	D0LHE3
D	Microcompartments protein	protein	199	34% helix, 30% strand	D0LHE3
E	Microcompartments protein	protein	195	33% helix, 30% strand	D0LHE3
F	Microcompartments protein	protein	197	36% helix, 30% strand	D0LHE3

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D, E, F

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

Pockets

16 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.47	0.83	14	empty
2	93	0.46	0.80	18	empty
3	77	0.46	0.82	17	empty
4	111	0.44	0.78	30	empty
5	69	0.40	0.80	15	empty

Interfaces

7 interfaces between chains.

B–C · 991 Å² buried · 18 hydrogen bonds · protein-protein
D–F · 897 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 885 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 885 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 870 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5DII · Structure of an engineered bacterial microcompartment shell protein binding a [4Fe-4S]… · the same entry in another collection · chain F against F, TM-score 1.00
D0LHE3 · AlphaFold monomer V2.0 prediction for bacterial microcompartment protein trimer-1 (D0LHE3) · a predicted model of the same protein · chain C 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
Every structure of UniProt D0LHE3
Elsewhere: RCSB PDB 5DII · PDBe 5DII · UniProt D0LHE3

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