MolNFT v1 · #127317 · protein

Human insulin in complex with serotonin and arginine

5MT3: “Human insulin in complex with serotonin and arginine”. X-ray diffraction, 4 ligands (SRO, ARG, ZN), 12 pockets (best druggability 0.82). MolNFT v1 #127317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MT3
Type: protein
Length: 754 residues
Chains: 32
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Insulin
UniProt: P01308
Ligands: SRO, ARG, ZN, CL
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 10 distinct chains · 58% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Insulin	protein	13	54% helix, 8% strand	P01308
B, Z, d	Insulin	protein	24	46% helix, 13% strand	P01308
C, G, I, M, O, Q, S, U, W, Y, a, c, e	Insulin	protein	21	48% helix, 14% strand	P01308
D	Insulin	protein	27	63% helix, 11% strand	P01308
E, K	Insulin	protein	20	65% helix, 5% strand	P01308
F, R, V	Insulin	protein	26	42% helix, 12% strand	P01308
H	Insulin	protein	28	75% helix, 11% strand	P01308
J, P, T, X, f	Insulin	protein	28	71% helix, 11% strand	P01308
L, N	Insulin	protein	27	41% helix, 11% strand	P01308
b	Insulin	protein	29	72% helix, 10% strand	P01308

Ligands and binding sites

SRO · Serotonin · ligand · 12 copies · chains C, D, E, O, P, Q, G, H, J, L, I, N, K, F, R, a, S, T, V, X, W, Z, b, c, d, f
ARG · Arginine · ligand · 4 copies · chains B, F, N, P, H, L, J
ZN · Zinc ion · metal · 8 copies · chains B, D, F, L, N, H, J, P, T, X, b, d, f
CL · Chloride ion · ion · 6 copies · chains B, D, F, L, N, H, J, P, T, X, b, f

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

Pockets

12 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	996	0.82	0.83	126	SRO, CL, ARG
2	337	0.79	0.90	46	SRO
3	339	0.72	0.84	56	SRO, ARG
4	441	0.71	0.81	58	SRO
5	296	0.69	0.83	46	SRO

Interfaces

96 interfaces between chains.

Q–R · 710 Å² buried · 7 hydrogen bonds · protein-protein
K–L · 673 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 662 Å² buried · 7 hydrogen bonds · protein-protein
M–N · 659 Å² buried · 6 hydrogen bonds · protein-protein
N–P · 645 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide (disulfide).

Compared structures

5MT3 · Human insulin in complex with serotonin and arginine · the same entry in another collection · chain M against M, 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 5MT3 · PDBe 5MT3 · UniProt P01308

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