6CWY: SUMO E1

Crystal structure of SUMO E1 in complex with an allosteric inhibitor. Determined by X-ray diffraction at 2.46 Å resolution. Released 16 Jan 2019.

Method: X-ray diffraction
Resolution: 2.46 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,335
Mol. weight: 113.07 kDa
Ligands: ZN, MG, FHJ
Released: 16 Jan 2019

Explore 6CWY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CWY contains 42 α-helices and 35 β-strands across 2 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 C: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	18-28	11
α-helix	30-35	6
β-strand	38-42	5	1
α-helix	46-58	13
β-strand	62-66	5	1
β-strand	70	1	2
α-helix	83	1
β-strand	90	1	2
α-helix	91-94	4
α-helix	96-102	7
β-strand	107-111	5	1
α-helix	115-117	3
α-helix	120-123	4
β-strand	128-132	5	1
α-helix	136-148	13
β-strand	152-159	8	1
β-strand	160	1	3
β-strand	162-168	7	1
β-strand	171-177	7	4
β-strand	206-212	7	4
α-helix	216-220	5
α-helix	227-235	9
α-helix	239-253	15
α-helix	262-279	18
α-helix	284-286	3
α-helix	289-293	5
β-strand	298	1	3
α-helix	300-319	20
β-strand	321	1	4
α-helix	323-325	3
β-strand	328-332	5	1
β-strand	337-341	5	1

Chain D: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
β-strand	7	1	5
α-helix	9-17	9
β-strand	19-23	5	1
α-helix	29-39	11
β-strand	43-47	5	1
α-helix	72-83	12
β-strand	88-91	4	1
α-helix	103-106	4
β-strand	111-114	4	1
α-helix	119-132	14
β-strand	136-142	7	1
β-strand	145-151	7	1
α-helix	165-167	3
β-strand	168-170	3	6
α-helix	172-176	5
α-helix	183-197	15
α-helix	202-204	3
α-helix	240-246	7
α-helix	251-258	8
α-helix	261-266	6
α-helix	270-272	3
α-helix	277-279	3
α-helix	284-287	4
α-helix	315-331	17
α-helix	349-365	17
α-helix	373-378	6
β-strand	383-385	3	6
α-helix	388-406	19
α-helix	410-412	3
β-strand	414-418	5	1
β-strand	427-433	7	1
α-helix	434-438	5
β-strand	449-454	6	7
β-strand	460	1	8
α-helix	461-463	3
α-helix	464-472	9
β-strand	479-482	4	7
β-strand	489-491	3	7
α-helix	499-501	3
β-strand	505	1	8
α-helix	506-509	4
β-strand	516-521	6	7
β-strand	526-534	9	7
β-strand	544-546	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-activating enzyme subunit 1	C	protein	346	Homo sapiens	Q9UBE0 (AlphaFold model)
SUMO-activating enzyme subunit 2	D	protein	660	Homo sapiens	Q9UBT2 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6CWY_1 SUMO-activating enzyme subunit 1 (chains C)
MVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGV
KGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPE
SFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTK
VAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDY
FLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMA
PVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK

Sequence of entity 2 (D), FASTA

>6CWY_2 SUMO-activating enzyme subunit 2 (chains D)
MGSSHHHHHHSSGLVPRGSHMALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTG
FSHIDLIDLDTIDVSNLNRQFLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPD
YNVEFFRQFILVMNALDNRAARNHVNRMCLAADVPLIESGTAGYLGQVTTIKKGVTECYE
CHPKPTQRTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPT
EAEARARASNEDGDIKRISTKEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPV
PLDWAEVQSQGEETNASDQQNEPQLGLKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGA
ELIWDKDDPSAMDFVTSAANLRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVL
EGLKILSGKIDQCRTIFLNKQPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVT
VLTLQDKIVKEKFAMVAPDVQIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQAD
DFLQDYTLLINILHSEDLGKDVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTST
AQEQDDVLIVDSDEEDSSNNADVSEEERSRKRKLDEKENLSAKRSRIEQKEELDDVIALD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1
FHJ	dimethyl (1S,2S,3R,4R)-1-[(1S)-2-(4-methylphenyl)-1-(phenylamino)ethyl]-7-oxabi…	C25 H27 N O5	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Molecular mechanism of a covalent allosteric inhibitor of SUMO E1 activating enzyme. Lv, Z., Yuan, L., Atkison, J.H. et al. Nat Commun (2018) 9:5145-5145. DOI 10.1038/s41467-018-07015-1 · PubMed

Other PDB entries of the same protein (UniProt Q9UBE0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QN5 1.97 Å, Crystal structure of human SUMO E1 with small unit cell parameters in the P1 21 1 space…
6XOG 1.98 Å, Structure of SUMO1-ML786519 adduct bound to SAE
6XOI 2.0 Å, Structure of SUMO1-ML00752641 adduct bound to SAE
8VY5 2.01 Å, Crystal structure of human SAE1
6XOH 2.23 Å, Structure of SUMO1-ML00789344 adduct bound to SAE
1Y8Q 2.25 Å, Sumo E1 activating enzyme SAE1-SAE2-MG-ATP complex
3KYC 2.45 Å, Human SUMO E1 complex with a SUMO1-AMP mimic
9IF6 2.51 Å, Crystal structure of human SUMO E1 with large unit cell parameters in the P1 21 1 space…
3KYD 2.61 Å, Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic
9DRJ 2.7 Å, Cryo-EM structure of a SUMO E1-E2-SUMO1 complex.
1Y8R 2.75 Å, Sumo E1 activating enzyme SAE1-SAE2-SUMO1-MG-ATP complex
6CWZ 3.1 Å, Crystal structure of apo SUMO E1

Browse structure collections

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