5DMZ: PDB entry 5DMZ

Structure of human Bub1 kinase domain phosphorylated at Ser969. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Dec 2015.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,606
Mol. weight: 84.75 kDa
Ligands: MG, ADP
Released: 16 Dec 2015

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

Secondary structure: helices and β-sheets

5DMZ contains 34 α-helices and 36 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 A: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	737-738	2	1
α-helix	744-752	9
α-helix	758-760	3
β-strand	764-766	3	2
α-helix	770-773	4
β-strand	778-781	4	2
β-strand	786-795	10	2
β-strand	800-805	6	2
β-strand	817-823	7	2
α-helix	828-840	13
α-helix	843-848	6
β-strand	849	1	3
α-helix	850-851	2
β-strand	852-857	6	2
β-strand	862-866	5	2
β-strand	873	1	3
α-helix	874-883	10
α-helix	891-910	20
β-strand	913-914	2	4
α-helix	920-922	3
β-strand	923-924	2	3
α-helix	927-930	4
β-strand	943-944	2	3
β-strand	951-952	2	4
α-helix	957	1
β-strand	961-962	2	1
α-helix	974-977	4
β-strand	982	1	1
α-helix	985-1000	16
β-strand	1006-1009	4	5
β-strand	1012-1015	4	5
α-helix	1025-1036	12
α-helix	1044-1046	3
α-helix	1047-1061	15
α-helix	1066-1082	17

Chain B: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	736-738	3	6
α-helix	744-752	9
α-helix	758-760	3
β-strand	764-767	4	7
α-helix	770-773	4
β-strand	779-782	4	7
β-strand	785-795	11	7
β-strand	799-805	7	7
β-strand	818-823	6	7
α-helix	828-840	13
α-helix	843-848	6
β-strand	849	1	8
β-strand	852-858	7	7
β-strand	862-866	5	7
β-strand	873	1	8
α-helix	874-883	10
α-helix	891-910	20
β-strand	913-914	2	9
α-helix	920-922	3
β-strand	923-924	2	8
α-helix	927-931	5
β-strand	943-944	2	8
β-strand	951-952	2	9
α-helix	957	1
β-strand	960-962	3	6
α-helix	974-977	4
β-strand	982	1	6
α-helix	985-1000	16
β-strand	1006-1009	4	10
β-strand	1012-1015	4	10
α-helix	1025-1036	12
α-helix	1041-1043	3
α-helix	1044-1046	3
α-helix	1047-1061	15
α-helix	1066-1081	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitotic checkpoint serine/threonine-protein kinase BUB1	A, B	protein	365	Homo sapiens	O43683 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5DMZ_1 Mitotic checkpoint serine/threonine-protein kinase BUB1 (chains A, B)
GPMDPSSLGTVDAPNFIVGNPWDDKLIFKLLSGLSKPVSSYPNTFEWQCKLPAIKPKTEF
QLGSKLVYVHHLLGEGAFAQVYEATQGDLNDAKNKQKFVLKVQKPANPWEFYIGTQLMER
LKPSMQHMFMKFYSAHLFQNGSVLVGELYSYGTLLNAINLYKNTPEKVMPQGLVISFAMR
MLYMIEQVHDCEIIHGDIKPDNFILGNGFLEQDDEDDLSAGLALIDLGQSIDMKLFPKGT
IFTAKCETSGFQCVEMLSNKPWNYQIDYFGVAATVYCMLFGTYMKVKNEGGECKPEGLFR
RLPHLDMWNEFFHVMLNIPDCHHLPSLDLLRQKLKKVFQQHYTNKIRALRNRLIVLLLEC
KRSRK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Primary citation

Role of Intrinsic and Extrinsic Factors in the Regulation of the Mitotic Checkpoint Kinase Bub1. Breit, C., Bange, T., Petrovic, A. et al. PLoS One (2015) 10:e0144673-e0144673. DOI 10.1371/journal.pone.0144673 · PubMed

Other PDB entries of the same protein (UniProt O43683 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7B1F 1.75 Å, Orthorhombic P212121 Structure of Human Mad1 C-terminal Domain in Complex with…
9RJ4 1.85 Å, Bub1 kinase domain in complex with inhibitor LEI221
6F7B 2.0 Å, Crystal structure of the human Bub1 kinase domain in complex with BAY 1816032
4QPM 2.2 Å, Structure of Bub1 kinase domain
9RJ2 2.3 Å, Bub1 kinase domain in complex with covalent inhibitor BM047
4R8Q 2.31 Å, Structure and substrate recruitment of the human spindle checkpoint kinase bub1
7B1H 2.4 Å, Monoclinic P21 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated…
4A1G 2.6 Å, The crystal structure of the human Bub1 TPR domain in complex with the KI motif of Knl1
7B1J 2.9 Å, Orthorhombic P21212 Structure of Human Mad1 C-terminal Domain in Complex with…
2LAH Solution NMR Structure of Mitotic checkpoint serine/threonine-protein kinase BUB1…

Browse structure collections

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