MolNFT v1 · #125244 · protein

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

5L39 · Rmm microcompartment shell protein MSM0275: “The structure of the fused permuted hexameric shell protein MSM0275 from the rmm microcompartment”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.75). MolNFT v1…

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

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.