6XOI: SUMO1-ML00752641 adduct

Structure of SUMO1-ML00752641 adduct bound to SAE. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 Mar 2021.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,165
Mol. weight: 122.04 kDa
Ligands: ZN, VBA
Released: 24 Mar 2021

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

Secondary structure: helices and β-sheets

6XOI contains 46 α-helices and 38 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: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
α-helix	20-35	16
β-strand	38-42	5	1
α-helix	46-58	13
β-strand	62-66	5	1
α-helix	69	1
β-strand	70	1	2
α-helix	71	1
β-strand	79	1	3
β-strand	82	1	3
β-strand	90	1	2
α-helix	93-101	9
β-strand	107-111	5	1
α-helix	115-117	3
α-helix	120-125	6
β-strand	128-131	4	1
α-helix	136-148	13
β-strand	152-159	8	1
β-strand	160	1	4
β-strand	162-168	7	1
β-strand	171-177	7	5
β-strand	206-212	7	5
α-helix	216-220	5
α-helix	227-234	8
α-helix	239-253	15
α-helix	259-261	3
α-helix	262-279	18
α-helix	284-286	3
α-helix	289-293	5
β-strand	298	1	4
α-helix	300-319	20
β-strand	321	1	5
α-helix	323-325	3
β-strand	328-332	5	1
β-strand	337-341	5	1

Chain B: 27 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
β-strand	20-23	4	1
α-helix	27-39	13
β-strand	44-48	5	1
β-strand	51	1	6
α-helix	54-58	5
α-helix	65-67	3
β-strand	71	1	6
α-helix	72-83	12
β-strand	89-93	5	1
α-helix	103-107	5
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	172-176	5
α-helix	182-197	16
α-helix	251-256	6
α-helix	257-261	5
α-helix	262-267	6
α-helix	272-274	3
α-helix	277-279	3
α-helix	284-287	4
α-helix	308-310	3
α-helix	311-314	4
α-helix	315-330	16
α-helix	349-365	17
α-helix	368-370	3
α-helix	373-381	9
α-helix	383-385	3
α-helix	388-406	19
α-helix	410-412	3
β-strand	415-418	4	1
β-strand	427-432	6	1
α-helix	433-438	6
β-strand	449-452	4	7
α-helix	463-464	2
α-helix	465-470	6
β-strand	520-521	2	8
β-strand	526-527	2	8
β-strand	529-532	4	7
β-strand	546	1	7

Chain C: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	23-27	5	9
β-strand	33-37	5	9
β-strand	63-65	3	9
β-strand	70	1	9
β-strand	88-91	4	9
α-helix	92-94	3
β-strand	96	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-activating enzyme subunit 1	A	protein	346	Homo sapiens	Q9UBE0 (AlphaFold model)
SUMO-activating enzyme subunit 2	B	protein	640	Homo sapiens	Q9UBT2 (AlphaFold model)
Small ubiquitin-related modifier 1	C	protein	101	Homo sapiens	P63165 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6XOI_1 SUMO-activating enzyme subunit 1 (chains A)
MVEKEEAGGGISEEEAAQYDRQIRLWGLEAQKRLRASRVLLVGLKGLGAEIAKNLILAGV
KGLTMLDHEQVTPEDPGAQFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPE
SFFTQFDAVCLTCCSRDVIVKVDQICHKNSIKFFTGDVFGYHGYTFANLGEHEFVEEKTK
VAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVKEALEVDWSSEKAKAALKRTTSDY
FLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLLPEDFVRYCFSEMA
PVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK

Sequence of entity 2 (B), FASTA

>6XOI_2 SUMO-activating enzyme subunit 2 (chains B)
MALSRGLPRELAEAVAGGRVLVVGAGGIGCELLKNLVLTGFSHIDLIDLDTIDVSNLNRQ
FLFQKKHVGRSKAQVAKESVLQFYPKANIVAYHDSIMNPDYNVEFFRQFILVMNALDNRA
ARNHVNRMCLAADVPLIESGTAGYLGQVTTIKKGVTECYECHPKPTQRTFPGCTIRNTPS
EPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPTEAEARARASNEDGDIKRIST
KEWAKSTGYDPVKLFTKLFKDDIRYLLTMDKLWRKRKPPVPLDWAEVQSQGEETNASDQQ
NEPQLGLKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGAELIWDKDDPSAMDFVTSAAN
LRMHIFSMNMKSRFDIKSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNK
QPNPRKKLLVPCALDPPNPNCYVCASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDV
QIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDFLQDYTLLINILHSEDLGK
DVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQDDVLIVDSDEEDSSNN
ADVSEEERSRKRKLDEKENLSAKRSRIEQKEELDDVIALD

Sequence of entity 3 (C), FASTA

>6XOI_3 Small ubiquitin-related modifier 1 (chains C)
MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMN
SLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
VBA	[(1R,2R,3S,4R)-4-{[5-(1-benzyl-1H-pyrazole-3-carbonyl)pyrimidin-4-yl]amino}-2,3…	C21 H24 N6 O6 S	1

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

Primary citation

Discovery of TAK-981, a First-in-Class Inhibitor of SUMO-Activating Enzyme for the Treatment of Cancer. Langston, S.P., Grossman, S., England, D. et al. J Med Chem (2021) 64:2501-2520. DOI 10.1021/acs.jmedchem.0c01491 · 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
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
6CWY 2.46 Å, Crystal structure of SUMO E1 in complex with an allosteric inhibitor
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

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