MolNFT v1 · #179688 · protein

Insulin receptor L1-cr plus alphact fragment in co-complex with fv 83- 7 and single-chain insulin sci-B

7KD6: “Insulin receptor L1-cr plus alphact fragment in co-complex with fv 83- 7 and single-chain insulin sci-B”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #179688 on GenesisL1: 3D…

PDB: 7KD6
Type: protein
Length: 2,324 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-chain insulin sci-B; Fv 83-7 heavy chain; Fv 83-7 light chain; Insulin receptor…
EC: 2.7.10.1
UniProt: P06213
Ligands: NAG, FUC, BMA, SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 15 distinct chains · 11% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Single-chain insulin sci-B	protein	49	47% helix, 4% strand	—
C, I	Fv 83-7 heavy chain	protein	123	5% helix, 46% strand	—
D, J	Fv 83-7 light chain	protein	115	3% helix, 52% strand	—
E	Insulin receptor subunit alpha (EC 2.7.10.1)	protein	286	13% helix, 30% strand	P06213
F, L, R	Insulin receptor isoform a alphact peptide (EC 2.7.10.1)	protein	15	60% helix, 0% strand	—
H, N	Single-chain insulin sci-B	protein	47	47% helix, 4% strand	—
K	Insulin receptor subunit alpha (EC 2.7.10.1)	protein	282	10% helix, 33% strand	P06213
O	Fv 83-7 heavy chain	protein	124	2% helix, 46% strand	—
P	Fv 83-7 light chain	protein	115	3% helix, 50% strand	—
Q	Insulin receptor subunit alpha (EC 2.7.10.1)	protein	290	10% helix, 31% strand	P06213
T	Single-chain insulin sci-B	protein	47	47% helix, 0% strand	—
U	Fv 83-7 heavy chain	protein	119	5% helix, 48% strand	—
V	Fv 83-7 light chain	protein	114	3% helix, 49% strand	—
W	Insulin receptor subunit alpha (EC 2.7.10.1)	protein	269	10% helix, 33% strand	P06213
X	Insulin receptor isoform a alphact peptide (EC 2.7.10.1)	protein	14	64% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains E, C, K, I, Q, O, W, U, N, T
FUC · alpha-L-fucopyranose · sugar · 6 copies · chains B, E, K, Q, W
BMA · beta-D-mannopyranose · sugar · 5 copies
SO4 · Sulfate ion · ion · 4 copies · chains C, E, I, K, O, Q, U, W
GOL · Glycerol · additive · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1044	0.84	0.85	104	empty
2	521	0.77	0.84	57	empty
3	914	0.76	0.79	91	NAG
4	461	0.76	0.85	48	empty
5	949	0.72	0.76	81	empty

Interfaces

45 interfaces between chains.

O–P · 897 Å² buried · 15 hydrogen bonds · protein-protein
U–V · 885 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 884 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 878 Å² buried · 17 hydrogen bonds · protein-protein
I–O · 752 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 73 disulfide, 20 glycan (disulfide, N-glycosylation).

Compared structures

7KD6 · Insulin Receptor L1-CR plus alphaCT fragment in co-complex with Fv 83-7 and single-chain… · the same entry in another collection · chain B against B, 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 P06213
Elsewhere: RCSB PDB 7KD6 · PDBe 7KD6 · UniProt P06213

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