2WBY: Human insulin-degrading enzyme

Crystal structure of human insulin-degrading enzyme in complex with insulin. Determined by X-ray diffraction at 2.6 Å resolution. Released 24 Mar 2009.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 16,926
Mol. weight: 238.09 kDa
Ligands: ZN
Released: 24 Mar 2009

Explore 2WBY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2WBY contains 123 α-helices and 72 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 58 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	47-50	4	1
α-helix	53-55	3
β-strand	63-69	7	1
β-strand	74-79	6	1
β-strand	85-92	8	1
α-helix	96-98	3
α-helix	106-113	8
α-helix	114-116	3
β-strand	118	1	2
α-helix	126-132	7
β-strand	137-142	6	1
β-strand	147-154	8	1
α-helix	155-157	3
α-helix	158-167	10
β-strand	172	1	2
α-helix	176-193	18
α-helix	197-207	11
α-helix	214-216	3
α-helix	223	1
α-helix	224-228	5
α-helix	229-232	4
α-helix	237-248	12
α-helix	251-253	3
β-strand	254-260	7	1
α-helix	264-275	12
α-helix	283-286	4
α-helix	295-297	3
β-strand	300-304	5	3
β-strand	312-319	8	3
α-helix	323-325	3
α-helix	330-338	9
α-helix	346-352	7
β-strand	359-367	9	3
β-strand	370-378	9	3
α-helix	381-384	4
α-helix	387-404	18
α-helix	408-423	16
α-helix	425-429	5
α-helix	430-440	11
α-helix	446-448	3
α-helix	461-468	8
α-helix	473-475	3
β-strand	477-481	5	3
α-helix	483-485	3
β-strand	491-492	2	3
β-strand	499-504	6	3
α-helix	505-506	2
α-helix	507-514	8
α-helix	516-518	3
α-helix	538-541	4
β-strand	549-553	5	4
β-strand	557-563	7	4
β-strand	571-579	9	4
α-helix	581-583	3
α-helix	587-613	27
β-strand	616-623	8	4
β-strand	626-634	9	4
α-helix	638-649	12
α-helix	656-672	17
α-helix	673-675	3
α-helix	678-690	13
β-strand	691	1	5
α-helix	697-704	8
α-helix	709-721	13
β-strand	722-723	2	6
β-strand	724-731	8	4
α-helix	735-753	19
β-strand	756-757	2	6
α-helix	758-759	2
α-helix	760-762	3
β-strand	768	1	5
β-strand	769	1	7
β-strand	775-782	8	8
β-strand	789-799	11	8
α-helix	802-819	18
α-helix	820-826	7
β-strand	833-840	8	8
β-strand	843-852	10	8
α-helix	856-876	21
α-helix	879-894	16
α-helix	895-897	3
α-helix	900-912	13
α-helix	920-928	9
α-helix	933-943	11
β-strand	952-959	8	8
α-helix	980-985	6
α-helix	987-989	3
β-strand	990-991	2	8
α-helix	992	1
α-helix	995-1000	6
β-strand	1004	1	7
α-helix	1005-1010	6

Chain B: 58 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	47-50	4	9
β-strand	63-69	7	9
β-strand	74-79	6	9
β-strand	85-92	8	9
α-helix	96-98	3
α-helix	106-113	8
β-strand	118	1	10
α-helix	126-132	7
β-strand	137-142	6	9
β-strand	147-154	8	9
α-helix	155-157	3
α-helix	158-166	9
α-helix	167-169	3
β-strand	172	1	10
α-helix	176-194	19
α-helix	197-208	12
α-helix	214-216	3
α-helix	223	1
α-helix	224-228	5
α-helix	229-232	4
α-helix	237-248	12
α-helix	251-253	3
β-strand	254-260	7	9
α-helix	264-275	12
α-helix	283-286	4
α-helix	295-297	3
β-strand	300-304	5	11
β-strand	312-320	9	11
α-helix	323-325	3
α-helix	330-338	9
α-helix	346-352	7
β-strand	359-367	9	11
β-strand	370-378	9	11
α-helix	381-385	5
α-helix	387-404	18
α-helix	408-424	17
α-helix	425-429	5
α-helix	430-440	11
α-helix	446-448	3
α-helix	461-468	8
α-helix	473-475	3
β-strand	477-481	5	11
α-helix	483-485	3
β-strand	491-492	2	11
β-strand	499-504	6	11
α-helix	505-506	2
α-helix	507-514	8
α-helix	524-527	4
α-helix	538-541	4
β-strand	549-553	5	12
β-strand	557-563	7	12
β-strand	571-579	9	12
α-helix	581-583	3
α-helix	587-613	27
β-strand	616-622	7	12
β-strand	626-634	9	12
α-helix	638-650	13
α-helix	656-671	16
α-helix	672-675	4
α-helix	678-690	13
β-strand	691	1	13
α-helix	697-704	8
α-helix	709-720	12
β-strand	722-723	2	14
β-strand	724-731	8	12
α-helix	735-753	19
β-strand	756-757	2	14
α-helix	758-759	2
α-helix	760-762	3
α-helix	765-767	3
β-strand	768	1	13
β-strand	769	1	15
β-strand	775-782	8	16
β-strand	789-799	11	16
α-helix	802-820	19
α-helix	821-826	6
β-strand	832-840	9	16
β-strand	843-852	10	16
α-helix	856-875	20
α-helix	879-894	16
α-helix	900-912	13
α-helix	920-929	10
α-helix	933-939	7
α-helix	940-944	5
β-strand	952-959	8	16
α-helix	981-985	5
α-helix	987-989	3
β-strand	990-991	2	16
α-helix	992	1
α-helix	995-1000	6
β-strand	1004	1	15
α-helix	1005-1009	5

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	3
α-helix	5-8	4
α-helix	13-17	5

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	9-17	9

Chain E: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	11
α-helix	5-8	4
α-helix	10-12	3
α-helix	13-17	5

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	9
α-helix	9-18	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Insulin-degrading enzyme	A, B	protein	990	HOMO SAPIENS	P14735 (AlphaFold model)
Insulin a chain	C, E	protein	20	HOMO SAPIENS	P01308 (AlphaFold model)
Insulin B chain	D, F	protein	19	HOMO SAPIENS	P01308 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2WBY_1 INSULIN-DEGRADING ENZYME (chains A, B)
MHHHHHHAAGIPMNNPAIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAA
LDVHIGSLSDPPNIAGLSHFLQHMLFLGTKKYPKENEYSQFLSEHAGSSNAFTSGEHTNY
YFDVSHEHLEGALDRFAQFFLSPLFDESAKDREVNAVDSEHEKNVMNDAWRLFQLEKATG
NPKHPFSKFGTGNKYTLETRPNQEGIDVRQELLKFHSAYYSSNLMAVVVLGRESLDDLTN
LVVKLFSEVENKNVPLPEFPEHPFQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSN
PGHYLGHLIGHEGPGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVED
IILHMFQYIQKLRAEGPQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILHYYPLEEV
LTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRTEEWYGTQYKQEAIPDEV
IKKWQNADLNGKFKLPTKNEFIPTNFEILPLEKEATPYPALIKDTAMSKLWFKQDDKFFL
PKANLNFEFFSPFAYVDPLHSNMAYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYL
SVKGYNDKQPILLKKIIEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLL
MTEVAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIMQMVEDTL
IEHAHTKPLLPSQLVRYREVQLPDRGWFVYQQRNEVHNNSGIEIYYQTDMQSTSENMFLE
LFAQIISEPAFNTLRTKEQLGYIVFSGPRRANGIQGLRFIIQSEKPPHYLESRVEAFLIT
MEKSIEDMTEEAFQKHIQALAIRRLDKPKKLSAESAKYWGEIISQQYNFDRDNTEVAYLK
TLTKEDIIKFYKEMLAVDAPRRHKVSVHVLAREMDSNPVVGEFPAQNDINLSQAPALPQP
EVIQNMTEFKRGLPLFPLVKPHINFMAAKL

Sequence of entity 2 (C, E), FASTA

>2WBY_2 INSULIN A CHAIN (chains C, E)
GIVEQCCTSICSLYQLENYC

Sequence of entity 3 (D, F), FASTA

>2WBY_3 INSULIN B CHAIN (chains D, F)
FVNQHLCGSHLVEALYLVC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Molecular Basis of Catalytic Chamber-Assisted Unfolding and Cleavage of Human Insulin by Human Insulin Degrading Enzyme. Manolopoulou, M., Guo, Q., Malito, E. et al. J Biol Chem (2009) 284:14177. DOI 10.1074/JBC.M900068200 · PubMed

Other PDB entries of the same protein (UniProt P14735 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3CWW 1.96 Å, Crystal Structure of IDE-bradykinin complex
2G47 2.1 Å, Crystal structure of human insulin-degrading enzyme in complex with amyloid-beta (1-40)
2G56 2.2 Å, crystal structure of human insulin-degrading enzyme in complex with insulin B chain
4PES 2.21 Å, Crystal structure of insulin degrading enzyme complexed with inhibitor tert-butyl…
4PFC 2.21 Å, Crystal structure of insulin degrading enzyme complexed with inhibitor
2G54 2.25 Å, Crystal structure of Zn-bound human insulin-degrading enzyme in complex with insulin B…
3E4Z 2.28 Å, Crystal structure of human insulin degrading enzyme in complex with insulin-like growth…
3E50 2.3 Å, Crystal structure of human insulin degrading enzyme in complex with transforming growth…
4PF7 2.33 Å, Crystal structure of insulin degrading enzyme complexed with inhibitor
3OFI 2.35 Å, Crystal structure of human insulin-degrading enzyme in complex with ubiquitin
2G49 2.5 Å, Crystal structure of human insulin-degrading enzyme in complex with glucagon
4PF9 2.5 Å, Crystal structure of insulin degrading enzyme complexed with inhibitor

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