MolNFT v1 · #125243 · protein

The structure of the hexagonal shell protein MSM0272 from the rmm microcompartment

5L38 · MSM0272 - rmm microcompartment shell protein: “The structure of the hexagonal shell protein MSM0272 from the rmm microcompartment”. X-ray diffraction, 2 ligands (NA, CL), 7 pockets (best druggability 0.40). MolNFT v1 #125243 on…

PDB: 5L38
Type: protein
Length: 1,057 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MSM0272 - rmm microcompartment shell protein
UniProt: A0QP49
Ligands: NA, CL
Pockets: 7 · best druggability 0.40

Structure

x-ray diffraction · 7 distinct chains · 38% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MSM0272 - rmm microcompartment shell protein	protein	91	38% helix, 36% strand	A0QP49
B, K, L	MSM0272 - rmm microcompartment shell protein	protein	86	37% helix, 37% strand	A0QP49
C, F, G	MSM0272 - rmm microcompartment shell protein	protein	90	39% helix, 37% strand	A0QP49
D, J	MSM0272 - rmm microcompartment shell protein	protein	89	36% helix, 36% strand	A0QP49
E	MSM0272 - rmm microcompartment shell protein	protein	85	41% helix, 39% strand	A0QP49
H	MSM0272 - rmm microcompartment shell protein	protein	88	40% helix, 38% strand	A0QP49
I	MSM0272 - rmm microcompartment shell protein	protein	87	37% helix, 37% strand	A0QP49

Ligands and binding sites

NA · Sodium ion · metal · 3 copies · chains A, B, G, H, I, J
CL · Chloride ion · ion · 2 copies · chains A, F, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	78	0.40	0.78	14	empty
2	116	0.38	0.74	22	empty
3	91	0.37	0.75	14	empty
4	71	0.37	0.77	14	empty
5	62	0.33	0.76	14	empty

Interfaces

13 interfaces between chains.

G–H · 1032 Å² buried · 11 hydrogen bonds · protein-protein
K–L · 1023 Å² buried · 12 hydrogen bonds · protein-protein
I–J · 1014 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1000 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 999 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5L38 · The structure of the hexagonal shell protein MSM0272 from the RMM microcompartment · 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 A0QP49
Elsewhere: RCSB PDB 5L38 · PDBe 5L38 · UniProt A0QP49

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