5D2M: SUMO-conjugating enzyme UBC9

Complex between human SUMO2-RANGAP1, UBC9 and ZNF451. Determined by X-ray diffraction at 2.4 Å resolution. Released 4 Nov 2015.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 7
Atoms: 7,146
Mol. weight: 100 kDa
Released: 4 Nov 2015

Explore 5D2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D2M contains 46 α-helices and 30 β-strands across 7 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	3-18	16
β-strand	25-30	6	1
β-strand	36-46	11	1
α-helix	47-48	2
β-strand	57-63	7	1
α-helix	64-65	2
α-helix	72-73	2
β-strand	74-77	4	1
α-helix	80-81	2
β-strand	86	1	2
β-strand	91	1	1
β-strand	92	1	2
β-strand	94	1	3
α-helix	95-97	3
α-helix	109-120	12
α-helix	131-139	9
α-helix	141-154	14

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	4
β-strand	28-33	6	4
α-helix	41-51	11
β-strand	58-62	5	4
β-strand	65-66	2	4
α-helix	67-68	2
β-strand	82-88	7	4
β-strand	92	1	3

Chain C: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	432-439	8
α-helix	443-448	6
α-helix	453-460	8
α-helix	466-477	12
α-helix	484-502	19
α-helix	509-519	11
α-helix	529-532	4
α-helix	536-546	11
α-helix	553-555	3
α-helix	556-564	9
α-helix	568-571	4
α-helix	574-584	11

Chain D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
β-strand	25-30	6	5
β-strand	36-46	11	5
α-helix	47-48	2
β-strand	57-63	7	5
α-helix	72-73	2
β-strand	74-77	4	5
α-helix	80-81	2
β-strand	86	1	6
β-strand	91	1	5
β-strand	92	1	6
β-strand	94	1	7
α-helix	95-97	3
α-helix	109-120	12
α-helix	131-139	9
α-helix	141-154	14

Chain E: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	8
β-strand	29-35	7	8
α-helix	41-51	11
α-helix	55-57	3
β-strand	58-62	5	8
β-strand	65-66	2	8
α-helix	67-68	2
β-strand	82-88	7	8
β-strand	92	1	7

Chain F: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	433-439	7
α-helix	443-448	6
α-helix	453-460	8
α-helix	466-477	12
α-helix	484-503	20
α-helix	509-519	11
α-helix	529-532	4
α-helix	536-546	11
α-helix	553-555	3
α-helix	556-564	9
α-helix	568-571	4
α-helix	574-584	11

Chain G: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	32-38	7	4
β-strand	42-47	6	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-conjugating enzyme UBC9	A, D	protein	161	Homo sapiens	P63279 (AlphaFold model)
Small ubiquitin-related modifier 2	B, E	protein	83	Homo sapiens	P61956 (AlphaFold model)
Ran GTPase-activating protein 1	C, F	protein	171	Homo sapiens	P46060 (AlphaFold model)
Zinc finger protein 451	G	protein	65	Homo sapiens	Q9Y4E5 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5D2M_1 SUMO-conjugating enzyme UBC9 (chains A, D)
GSHMSGIALSRLAQERRAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGL
FKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQ
ELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS

Sequence of entity 2 (B, E), FASTA

>5D2M_2 Small ubiquitin-related modifier 2 (chains B, E)
GSHMNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINET
DTPAQLEMEDEDTIDVFQQQTGG

Sequence of entity 3 (C, F), FASTA

>5D2M_3 Ran GTPase-activating protein 1 (chains C, F)
SNTGEPAPVLSSPPPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKV
SSVFKDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLY
GPLMALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV

Sequence of entity 4 (G), FASTA

>5D2M_4 Zinc finger protein 451 (chains G)
GAMDHVEFGSGDPGSEIIESVPPAGPEASESTTDENEDDIQFVSEGPLRPVLEYIDLVSS
DDEEP

Primary citation

Structural basis for catalytic activation by the human ZNF451 SUMO E3 ligase. Cappadocia, L., Pichler, A., Lima, C.D. Nat Struct Mol Biol (2015) 22:968-975. DOI 10.1038/nsmb.3116 · PubMed

Other PDB entries of the same protein (UniProt P63279 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5F6E 1.12 Å, Crystal Structure of human Ubc9 (K48A/K49A/E54A)
5F6Y 1.14 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)
2GRR 1.3 Å, Crystal Structure of human RanGAP1-Ubc9-D127S
5F6V 1.49 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from…
5F6U 1.55 Å, Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)
5F6D 1.55 Å, Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6
5F6X 1.56 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole…
5F6W 1.7 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol)
2GRO 1.7 Å, Crystal Structure of human RanGAP1-Ubc9-N85Q
2GRQ 1.7 Å, Crystal Structure of human RanGAP1-Ubc9-D127A
9GLR 1.72 Å, Crystal Structure of Human UBC9 C93E
2GRN 1.8 Å, Crystal Structure of human RanGAP1-Ubc9

Browse structure collections

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