7ZLN: SOCS2:ElonginB:ElonginC

Name: PDB 7ZLN: Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 11
Published: 2023-04-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 11. Determined by X-ray diffraction at 2.6 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,682
Mol. weight: 43.91 kDa
Ligands: JI9
Released: 26 Apr 2023

Explore 7ZLN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZLN contains 22 α-helices and 20 β-strands across 3 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	31-43	13
β-strand	49	1	1
α-helix	55-61	7
α-helix	66	1
β-strand	70-74	5	1
β-strand	82-88	7	1
β-strand	91-96	6	1
β-strand	97-99	3	2
β-strand	104-106	3	2
α-helix	113-115	3
β-strand	119	1	2
α-helix	122-134	13
α-helix	142-143	2
β-strand	155	1	1
α-helix	163-172	10
α-helix	178-180	3
α-helix	185-193	9

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	3
β-strand	14-19	6	3
β-strand	23	1	4
α-helix	24-35	12
α-helix	39-41	3
β-strand	44-46	3	3
β-strand	49-50	2	3
β-strand	56	1	4
α-helix	58-60	3
β-strand	68	1	5
β-strand	71	1	5
α-helix	72	1
β-strand	73-77	5	3
α-helix	85-87	3
α-helix	94-96	3
α-helix	98-100	3
α-helix	101-103	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	3
β-strand	28-32	5	3
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	3
α-helix	67-82	16
α-helix	90-92	3
α-helix	97-110	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Suppressor of cytokine signaling 2	A	protein	169	Homo sapiens	O14508 (AlphaFold model)
Elongin-B	B	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	C	protein	97	Homo sapiens	Q15369 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7ZLN_1 Suppressor of cytokine signaling 2 (chains A)
SMQAARLAKALRELGQTGWYWGSMTVNEAKEKLKEAPEGTFLIRDSSHSDYLLTISVKTS
AGPTNLRIEYQDGKFRLDSIICVKSKLKQFDSVVHLIDYYVQMCKDKRTGPEAPRNGTVH
LYLTKPLYTSAPSLQHLCRLTINKCTGAIWGLPLPTRLKDYLEEYKFQV

Sequence of entity 2 (B), FASTA

>7ZLN_2 Elongin-B (chains B)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 3 (C), FASTA

>7ZLN_3 Elongin-C (chains C)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Ligands and cofactors

ID	Name	Formula	Copies
JI9	[4-[(2~{S})-3-[(4-fluoranyl-3-methyl-phenyl)methylamino]-2-[2-(4-fluorophenyl)e…	C25 H25 F2 N2 O6 P	1

Primary citation

Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2. Ramachandran, S., Makukhin, N., Haubrich, K. et al. Nat Commun (2023) 14:6345-6345. DOI 10.1038/s41467-023-41894-3 · PubMed

Other PDB entries of the same protein (UniProt O14508 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
2C9W 1.9 Å, Crystal structure of socs-2 in complex with elongin-B and elongin-C at 1.9A resolution
7ZLS 1.92 Å, co-crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 13
7ZLP 1.94 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 9
6I5N 1.98 Å, Crystal structure of SOCS2:Elongin C:Elongin B in complex with growth hormone receptor…
7ZLR 2.01 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 13
7ZLO 2.22 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 12
6I4X 2.69 Å, Crystal structure of SOCS2:Elongin C:Elongin B in complex with erythropoietin receptor…
6I5J 2.8 Å, Crystal structure of SOCS2:Elongin C:Elongin B in complex with growth hormone receptor…
5BO4 2.9 Å, Structure of SOCS2:Elongin C:Elongin B from DMSO-treated crystals
4JGH 3.0 Å, Structure of the SOCS2-Elongin BC complex bound to an N-terminal fragment of Cullin5
7M6T 3.19 Å, Crystal structure of SOCS2/ElonginB/ElonginC bound to a non-canonical peptide that…

Browse structure collections

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