MolNFT v1 · #117925 · protein

Crystal structure of an iodinated insulin analog

5EMS: “Crystal structure of an iodinated insulin analog”. X-ray diffraction, 3 ligands (IPH, ZN, CL), 11 pockets (best druggability 0.83). MolNFT v1 #117925 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EMS
Type: protein
Length: 291 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Insulin
UniProt: P01308
Ligands: IPH, ZN, CL
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 64% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, I, K	Insulin	protein	21	52% helix, 5% strand	P01308
B, F, H, L	Insulin	protein	28	64% helix, 11% strand	P01308
D	Insulin	protein	26	62% helix, 12% strand	P01308
J	Insulin	protein	27	74% helix, 11% strand	P01308

Ligands and binding sites

IPH · Phenol · ligand · 6 copies · chains A, B, F, H, C, D, J, L, E, G, I, K
ZN · Zinc ion · metal · 2 copies · chains B, F, J, D, H, L
CL · Chloride ion · ion · 2 copies · chains D, H, L, B, F, J

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

Pockets

11 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	282	0.83	0.94	51	IPH
2	165	0.79	0.94	32	IPH
3	96	0.72	0.94	19	IPH
4	154	0.61	0.84	29	IPH
5	144	0.49	0.78	25	CL

Interfaces

39 interfaces between chains.

F–H · 728 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 718 Å² buried · 12 hydrogen bonds · protein-protein
J–L · 716 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 577 Å² buried · 8 hydrogen bonds · protein-protein
K–L · 566 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 6 modified (disulfide, nonstandard).

Compared structures

5EMS · Crystal Structure of an iodinated insulin analog · 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 5EMS · PDBe 5EMS · UniProt P01308

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