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Crystal structure of designed two-component self-assembling icosahedral cage I52-32

Analyse Crystal structure of designed two-component self-assembling icosahedral cage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IM4
Type: protein
Length: 5,302 residues
Chains: 40
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6,7-dimethyl-8-ribityllumazine synthase; Phosphotransferase system…
EC: 2.5.1.78
UniProt: A0A0A3CUI3, Q8RD55
Pockets: 20 · best druggability 0.67

Structure

x-ray diffraction · 16 distinct chains · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	135	48% helix, 20% strand	A0A0A3CUI3
E, e	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	133	49% helix, 20% strand	A0A0A3CUI3
C, B	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	137	47% helix, 20% strand	A0A0A3CUI3
D, X	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	132	49% helix, 20% strand	A0A0A3CUI3
F, H, G, I, J, P, Q, S, R, T, b, d, c, Z, a, j, k, m, l, n	Phosphotransferase system, MANNOSE/FRUCTOSE-specific component iia	protein	131	50% helix, 19% strand	Q8RD55
K, Y	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	135	48% helix, 20% strand	A0A0A3CUI3
L	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	136	48% helix, 20% strand	A0A0A3CUI3
N	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	134	49% helix, 20% strand	A0A0A3CUI3
M	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	139	50% helix, 19% strand	A0A0A3CUI3
O, g	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	130	50% helix, 19% strand	A0A0A3CUI3
U	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	134	49% helix, 20% strand	A0A0A3CUI3
V	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	136	48% helix, 20% strand	A0A0A3CUI3
W	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	132	49% helix, 20% strand	A0A0A3CUI3
f	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	134	49% helix, 20% strand	A0A0A3CUI3
h	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	133	49% helix, 20% strand	A0A0A3CUI3
i	6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78)	protein	135	48% helix, 20% strand	A0A0A3CUI3

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	307	0.67	0.82	24	empty
2	301	0.67	0.82	24	empty
3	326	0.66	0.81	22	empty
4	304	0.66	0.82	25	empty
5	572	0.65	0.76	66	empty

Interfaces

59 interfaces between chains.

Q–k · 1661 Å² buried · 19 hydrogen bonds · protein-protein
F–S · 1622 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 1028 Å² buried · 8 hydrogen bonds · protein-protein
C–B · 1017 Å² buried · 8 hydrogen bonds · protein-protein
V–W · 1016 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5IM4 · Crystal structure of designed two-component self-assembling icosahedral cage I52-32 · the same entry in another collection · chain E against E, 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 A0A0A3CUI3
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Elsewhere: RCSB PDB 5IM4 · PDBe 5IM4 · UniProt A0A0A3CUI3 · UniProt Q8RD55

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