Research workbench

Human insulin with intra-chain chemical crosslink between modified B27 and B30

Analyse Human insulin with intra-chain chemical crosslink between modified B27 and B30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BQQ
Type: protein
Length: 303 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Insulin
UniProt: P01308
Ligands: IPH, ZN, CL
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Insulin	protein	21	57% helix, 5% strand	P01308
B	Insulin	protein	27	74% helix, 11% strand	P01308
D, F, H, J, L	Insulin	protein	30	67% helix, 10% strand	P01308

Ligands and binding sites

IPH · Phenol · ligand · 10 copies · chains A, B, F, H, C, D, J, L, E, G, K, I
ZN · Zinc ion · metal · 2 copies · chains B, F, J, D, H, L
CL · Chloride ion · ion · 2 copies · chains B, F, J, D, H, L

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	475	0.84	0.91	56	IPH
2	188	0.70	0.87	39	IPH
3	179	0.69	0.87	27	IPH
4	184	0.68	0.86	28	IPH
5	102	0.37	0.74	25	empty

Interfaces

39 interfaces between chains.

J–L · 765 Å² buried · 10 hydrogen bonds · protein-protein
F–H · 754 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 654 Å² buried · 12 hydrogen bonds · protein-protein
K–L · 599 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 596 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 11 modified (disulfide, nonstandard).

Compared structures

5BQQ · Human insulin with intra-chain chemical crosslink between modified B27 and B30 · 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 P01308
Elsewhere: RCSB PDB 5BQQ · PDBe 5BQQ · UniProt P01308

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