9BDJ: Catalase

MicroED structure of bovine liver catalase with missing cone eliminated by suspended drop. Determined by electron crystallography at 4.0 Å resolution. Released 18 Sept 2024.

Method: Electron crystallography
Resolution: 4.0 Å
Organism: Bos taurus
Chains: 4
Atoms: 16,432
Mol. weight: 245.44 kDa
Ligands: HEM, NDP
Released: 18 Sept 2024

Explore 9BDJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BDJ contains 110 α-helices and 88 β-strands across 4 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: 27 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	22-24	3
β-strand	25	1	1
α-helix	26	1
β-strand	27	1	2
α-helix	32	1
β-strand	33	1	2
α-helix	34	1
β-strand	42-43	2	3
β-strand	49	1	3
β-strand	50	1	4
α-helix	54-63	10
α-helix	69-71	3
β-strand	77-86	10	5
α-helix	97-99	3
β-strand	105-113	9	5
β-strand	130-137	8	5
β-strand	140-147	8	5
α-helix	160-167	8
β-strand	169	1	6
β-strand	176	1	6
α-helix	178-187	10
α-helix	189-191	3
α-helix	192-198	7
α-helix	201-203	3
β-strand	205	1	7
β-strand	213-214	2	5
β-strand	219-222	4	5
β-strand	228-237	10	5
β-strand	243	1	7
α-helix	246-255	10
α-helix	259-269	11
β-strand	275-283	9	5
α-helix	285-288	4
β-strand	310-319	10	5
α-helix	324	1
α-helix	325-329	5
β-strand	342-344	3	5
α-helix	348-364	17
α-helix	369-371	3
β-strand	412	1	8
α-helix	415-417	3
α-helix	418-420	3
β-strand	422-430	9	9
α-helix	440-444	5
α-helix	445-449	5
α-helix	452-466	15
α-helix	471-482	12
α-helix	486-499	14

Chain B: 29 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	23-24	2
β-strand	25	1	10
α-helix	26	1
β-strand	27	1	11
α-helix	32	1
β-strand	33	1	11
α-helix	34	1
β-strand	41-43	3	3
β-strand	49	1	3
β-strand	50	1	4
α-helix	54-64	11
α-helix	69-71	3
β-strand	77-86	10	12
α-helix	97-99	3
β-strand	105-113	9	12
β-strand	130-137	8	12
β-strand	140-147	8	12
α-helix	157-159	3
α-helix	160-167	8
β-strand	169	1	13
β-strand	176	1	13
α-helix	178-187	10
α-helix	189-191	3
α-helix	192-198	7
α-helix	201-203	3
β-strand	205	1	14
β-strand	213-214	2	12
β-strand	219-222	4	12
β-strand	228-237	10	12
β-strand	243	1	14
α-helix	246-255	10
α-helix	259-269	11
β-strand	275-284	10	12
α-helix	285-290	6
β-strand	310-319	10	12
α-helix	324	1
α-helix	325-329	5
β-strand	342-344	3	12
α-helix	348-364	17
α-helix	369-371	3
α-helix	373-375	3
β-strand	412	1	15
α-helix	415-417	3
α-helix	418-421	4
β-strand	422-430	9	9
α-helix	440-444	5
α-helix	445-449	5
α-helix	452-466	15
α-helix	471-484	14
α-helix	486-499	14

Chain C: 28 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	22-24	3
β-strand	25	1	8
α-helix	26	1
β-strand	27	1	16
α-helix	32	1
β-strand	33	1	16
α-helix	34	1
β-strand	41-43	3	9
β-strand	49	1	9
β-strand	50	1	17
α-helix	54-64	11
α-helix	69-71	3
β-strand	77-86	10	18
α-helix	97-99	3
β-strand	105-113	9	18
β-strand	130-137	8	18
β-strand	140-147	8	18
α-helix	157-159	3
α-helix	160-167	8
β-strand	169	1	19
β-strand	176	1	19
α-helix	178-187	10
α-helix	189-191	3
α-helix	192-198	7
α-helix	201-203	3
β-strand	205	1	20
β-strand	213-214	2	18
β-strand	219-222	4	18
β-strand	228-237	10	18
β-strand	243	1	20
α-helix	246-255	10
α-helix	259-269	11
β-strand	275-283	9	18
α-helix	285-289	5
β-strand	310-319	10	18
α-helix	324	1
α-helix	325-329	5
β-strand	342-344	3	18
α-helix	348-364	17
α-helix	369-371	3
β-strand	412	1	1
α-helix	415-417	3
α-helix	418-421	4
β-strand	422-430	9	3
α-helix	440-444	5
α-helix	445-449	5
α-helix	452-466	15
α-helix	471-482	12
α-helix	486-499	14

Chain D: 26 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	22-24	3
β-strand	25	1	15
α-helix	26	1
β-strand	27	1	21
β-strand	33	1	21
β-strand	41-43	3	9
β-strand	49	1	9
β-strand	50	1	17
α-helix	54-64	11
α-helix	69-71	3
β-strand	77-86	10	22
α-helix	97-99	3
β-strand	105-113	9	22
β-strand	130-137	8	22
β-strand	140-147	8	22
α-helix	157-159	3
α-helix	160-167	8
β-strand	169	1	23
β-strand	176	1	23
α-helix	178-187	10
α-helix	189-191	3
α-helix	192-198	7
α-helix	201-203	3
β-strand	205	1	24
β-strand	213-214	2	22
β-strand	219-222	4	22
β-strand	228-237	10	22
β-strand	243	1	24
α-helix	246-255	10
α-helix	259-269	11
β-strand	275-283	9	22
α-helix	285-289	5
β-strand	310-319	10	22
α-helix	324	1
α-helix	325-329	5
β-strand	342-344	3	22
α-helix	348-364	17
α-helix	369-371	3
β-strand	412	1	10
α-helix	415-417	3
α-helix	418-420	3
β-strand	422-429	8	3
α-helix	440-444	5
α-helix	445-449	5
α-helix	452-466	15
α-helix	471-482	12
α-helix	486-499	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Catalase	A, B, C, D	protein	527	Bos taurus	P00432 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9BDJ_1 Catalase (chains A, B, C, D)
MADNRDPASDQMKHWKEQRAAQKPDVLTTGGGNPVGDKLNSLTVGPRGPLLVQDVVFTDE
MAHFDRERIPERVVHAKGAGAFGYFEVTHDITRYSKAKVFEHIGKRTPIAVRFSTVAGES
GSADTVRDPRGFAVKFYTEDGNWDLVGNNTPIFFIRDALLFPSFIHSQKRNPQTHLKDPD
MVWDFWSLRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNANGEAVYCKFHYKTDQ
GIKNLSVEDAARLAHEDPDYGLRDLFNAIATGNYPSWTLYIQVMTFSEAEIFPFNPFDLT
KVWPHGDYPLIPVGKLVLNRNPVNYFAEVEQLAFDPSNMPPGIEPSPDKMLQGRLFAYPD
THRHRLGPNYLQIPVNCPYRARVANYQRDGPMCMMDNQGGAPNYYPNSFSAPEHQPSALE
HRTHFSGDVQRFNSANDDNVTQVRTFYLKVLNEEQRKRLCENIAGHLKDAQLFIQKKAVK
NFSDVHPEYGSRIQALLDKYNEEKPKNAVHTYVQHGSHLSAREKANL

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4
NDP	NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate	C21 H30 N7 O17 P3	4

Primary citation

Eliminating the missing cone challenge through innovative approaches. Gillman, C., Bu, G., Danelius, E. et al. J Struct Biol X (2024) 9:100102-100102. DOI 10.1016/j.yjsbx.2024.100102 · PubMed

Other PDB entries of the same protein (UniProt P00432 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PO0 1.75 Å, The structure of the orthorhombic (P212121) crystal form of beef liver catalase at 1.85…
6PM7 1.85 Å, The structure of the triclinic crystal form of beef liver catalase at 1.85 A resolution
3RGP 1.88 Å, Structural and Kinetic Analysis of the Beef liver Catalase complexed with Nitric Oxide
3RE8 1.9 Å, Structural and Kinetic Analysis of the Beef liver Catalase interacting with Nitric Oxide
3RGS 1.99 Å, Structural and kinetic analysis of the beef liver catalase with the ammonia as a ligand
4BLC 2.3 Å, The structure of orthorhombic crystals of beef liver catalase
7CAT 2.5 Å, The NADPH binding site on beef liver catalase
8CAT 2.5 Å, The NADPH binding site on beef liver catalase
3NWL 2.69 Å, The crystal structure of the P212121 form of bovine liver catalase previously…
1TGU 2.8 Å, The crystal structure of bovine liver catalase without NADPH
1TH2 2.8 Å, crystal structure of NADPH depleted bovine liver catalase complexed with azide
1TH3 2.8 Å, Crystal structure of NADPH depleted bovine live catalase complexed with cyanide

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