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The structure of the fused permuted hexameric shell protein MSM0275 from the rmm microcompartment

Analyse The structure of the fused permuted hexameric shell protein MSM0275 from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L39
Type: protein
Length: 1,205 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rmm microcompartment shell protein MSM0275
UniProt: A0QP52
Ligands: CL
Pockets: 15 · best druggability 0.75

Structure

x-ray diffraction · 6 distinct chains · 39% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rmm microcompartment shell protein MSM0275	protein	208	42% helix, 28% strand	A0QP52
B	Rmm microcompartment shell protein MSM0275	protein	209	41% helix, 28% strand	A0QP52
C	Rmm microcompartment shell protein MSM0275	protein	196	37% helix, 30% strand	A0QP52
D	Rmm microcompartment shell protein MSM0275	protein	192	36% helix, 31% strand	A0QP52
E	Rmm microcompartment shell protein MSM0275	protein	198	38% helix, 30% strand	A0QP52
F	Rmm microcompartment shell protein MSM0275	protein	202	38% helix, 29% strand	A0QP52

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, D

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	922	0.75	0.79	83	empty
2	769	0.74	0.79	87	empty
3	342	0.60	0.77	51	empty
4	162	0.57	0.81	37	empty
5	88	0.54	0.84	14	empty

Interfaces

13 interfaces between chains.

B–C · 1033 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1014 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1002 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 971 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 933 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5L39 · The structure of the fused permuted hexameric shell protein MSM0275 from the RMM… · 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
Every structure of UniProt A0QP52
Elsewhere: RCSB PDB 5L39 · PDBe 5L39 · UniProt A0QP52

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