7ZLS: Co-crystal structure of SOCS2:ElonginB:ElonginC

Name: PDB 7ZLS: co-crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 13
Published: 2023-04-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

co-crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 13. Determined by X-ray diffraction at 1.92 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 12
Atoms: 11,373
Mol. weight: 175.82 kDa
Ligands: JH9
Released: 26 Apr 2023

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

Secondary structure: helices and β-sheets

7ZLS contains 84 α-helices and 90 β-strands across 12 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	33-46	14
β-strand	49	1	1
α-helix	55-62	8
α-helix	66	1
β-strand	70-74	5	1
β-strand	82-88	7	1
β-strand	91-100	10	1
β-strand	103-106	4	1
α-helix	113-115	3
β-strand	119	1	1
α-helix	122-134	13
β-strand	155	1	1
α-helix	160-162	3
α-helix	163-174	12
α-helix	178-180	3
α-helix	185-192	8

Chain B: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	2
β-strand	10	1	3
β-strand	12-19	8	2
β-strand	23	1	4
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	2
β-strand	49-50	2	2
α-helix	51-52	2
β-strand	56	1	4
α-helix	64-66	3
β-strand	68	1	5
β-strand	71	1	5
α-helix	72	1
β-strand	73-79	7	2
β-strand	80-81	2	6
β-strand	84-85	2	6
α-helix	86-88	3
β-strand	90	1	3
α-helix	91-100	10
α-helix	101-103	3

Chains C and I: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	2
β-strand	28-32	5	2
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	2
α-helix	67-82	16
α-helix	89-92	4
α-helix	97-110	14

Chain D: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	33-46	14
β-strand	49	1	7
α-helix	55-62	8
α-helix	66	1
β-strand	70-74	5	7
β-strand	82-88	7	7
β-strand	91-100	10	7
β-strand	103-106	4	7
β-strand	119	1	7
α-helix	122-133	12
β-strand	155	1	7
α-helix	160-162	3
α-helix	163-174	12
α-helix	178-180	3
α-helix	185-192	8

Chain E: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	10	1	9
β-strand	12-19	8	8
β-strand	23	1	10
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	8
β-strand	49-50	2	8
β-strand	56	1	10
α-helix	58-60	3
β-strand	68	1	11
β-strand	71	1	11
α-helix	72	1
β-strand	73-79	7	8
β-strand	80-81	2	12
β-strand	84-85	2	12
α-helix	86-88	3
β-strand	90	1	9
α-helix	91-94	4
α-helix	98-100	3
α-helix	101-103	3

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	8
β-strand	28-32	5	8
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	8
α-helix	67-82	16
α-helix	89-92	4
α-helix	97-110	14

Chain G: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	33-45	13
β-strand	49	1	18
α-helix	55-62	8
α-helix	66	1
β-strand	70-74	5	18
β-strand	82-88	7	18
β-strand	91-100	10	18
β-strand	103-106	4	18
α-helix	113-115	3
β-strand	119	1	18
α-helix	122-134	13
β-strand	155	1	18
α-helix	160-162	3
α-helix	163-174	12
α-helix	178-180	3
α-helix	185-192	8

Chain H: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	19
β-strand	10	1	20
β-strand	12-19	8	19
β-strand	23	1	21
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	19
β-strand	49-50	2	19
α-helix	51-52	2
β-strand	56	1	21
β-strand	68	1	22
β-strand	71	1	22
α-helix	72	1
β-strand	73-79	7	19
β-strand	80-81	2	23
β-strand	84-85	2	23
α-helix	86-88	3
β-strand	90	1	20
α-helix	91-100	10
α-helix	101-103	3

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Suppressor of cytokine signaling 2	A, D, G, J	protein	169	Homo sapiens	O14508 (AlphaFold model)
Elongin-B	B, E, H, K	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	C, F, I, L	protein	97	Homo sapiens	Q15369 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>7ZLS_1 Suppressor of cytokine signaling 2 (chains A, D, G, J)
SMQAARLAKALRELGQTGWYWGSMTVNEAKEKLKEAPEGTFLIRDSSHSDYLLTISVKTS
AGPTNLRIEYQDGKFRLDSIICVKSKLKQFDSVVHLIDYYVQMCKDKRTGPEAPRNGTVH
LYLTKPLYTSAPSLQHLCRLTINKCTGAIWGLPLPTRLKDYLEEYKFQV

Sequence of entity 2 (B, E, H, K), FASTA

>7ZLS_2 Elongin-B (chains B, E, H, K)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 3 (C, F, I, L), FASTA

>7ZLS_3 Elongin-C (chains C, F, I, L)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Ligands and cofactors

ID	Name	Formula	Copies
JH9	[4-[(2~{S})-3-[(4-fluoranyl-3-prop-2-enyl-phenyl)methylamino]-2-[2-(4-fluorophe…	C27 H27 F2 N2 O6 P	4

Water and common crystallization additives (EDO) are not listed.

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
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
7ZLN 2.6 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 11
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…

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