3IBF: Unliganded caspase-7

Crystal structure of unliganded caspase-7. Determined by X-ray diffraction at 2.5 Å resolution. Released 1 Sept 2009.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,804
Mol. weight: 61.83 kDa
Released: 1 Sept 2009

Explore 3IBF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3IBF contains 22 α-helices and 38 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: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	59	1	1
β-strand	66-74	9	2
α-helix	80-82	3
α-helix	84-86	3
α-helix	90-104	15
β-strand	106-112	7	2
α-helix	116-128	13
β-strand	134-142	9	2
β-strand	145-146	2	3
β-strand	149-151	3	3
β-strand	156-158	3	3
α-helix	159-163	5
α-helix	164-166	3
α-helix	168-170	3
α-helix	172-174	3
β-strand	179-184	6	2
β-strand	190	1	4
β-strand	192	1	5
β-strand	195	1	6

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	213	1	7
β-strand	219-223	5	2
β-strand	229	1	4
α-helix	230-232	3
β-strand	233-234	2	8
β-strand	238-239	2	8
α-helix	240-252	13
α-helix	258-270	13
α-helix	280-282	3
β-strand	286	1	5
β-strand	290-293	4	2
β-strand	298	1	1

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	359	1	9
β-strand	366-374	9	2
α-helix	380-382	3
α-helix	384-386	3
α-helix	390-403	14
β-strand	407-412	6	2
α-helix	416-427	12
β-strand	434-442	9	2
β-strand	445-446	2	10
β-strand	449-451	3	10
β-strand	456-458	3	10
α-helix	459-464	6
α-helix	472-474	3
β-strand	479-484	6	2
β-strand	490	1	11
α-helix	491	1
β-strand	492	1	12
β-strand	495	1	7

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	513	1	6
β-strand	519-523	5	2
β-strand	529	1	11
β-strand	533-534	2	13
β-strand	538-539	2	13
α-helix	540-552	13
α-helix	558-570	13
α-helix	580-582	3
β-strand	586	1	12
β-strand	590-593	4	2
β-strand	598	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Caspase-7	A, C	protein	173	Homo sapiens	P55210 (AlphaFold model)
Caspase-7	B, D	protein	97	Homo sapiens	P55210 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3IBF_1 Caspase-7 (chains A, C)
AKPDRSSFVPSLFSKKKKNVTMRSIKTTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTG
MGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLS
HGEENVIYGKDGVTPIKDLTAHFRGDRCKTLLEKPKLFFIQACRGTELDDGIQ

Sequence of entity 2 (B, D), FASTA

>3IBF_2 Caspase-7 (chains B, D)
ANPRYKIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVN
DRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ

Primary citation

Conformational similarity in the activation of caspase-3 and -7 revealed by the unliganded and inhibited structures of caspase-7. Agniswamy, J., Fang, B., Weber, I.T. Apoptosis (2009) 14:1135-1144. DOI 10.1007/s10495-009-0388-9 · PubMed

Other PDB entries of the same protein (UniProt P55210 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JR2 1.65 Å, Human procaspase-7/caspase-7 heterodimer bound to Ac-DEVD-CMK
4JB8 1.7 Å, Caspase-7 in Complex with DARPin C7_16
2QL9 2.14 Å, Crystal Structure of Caspase-7 with inhibitor AC-DQMD-CHO
4JR1 2.15 Å, Human procaspase-7 bound to Ac-DEVD-CMK
5K20 2.2 Å, Caspase-7 S239E Phosphomimetic
2QLB 2.25 Å, Crystal Structure of caspase-7 with inhibitor AC-ESMD-CHO
4LSZ 2.26 Å, Caspase-7 in Complex with DARPin D7.18
4ZVR 2.3 Å, Caspase-7 Variant 4 (V4) with reprogrammed substrate specificity due to…
2QL5 2.34 Å, Crystal Structure of caspase-7 with inhibitor AC-DMQD-CHO
1F1J 2.35 Å, Crystal structure of caspase-7 in complex with acetyl-asp-glu-val-asp-cho
6CL2 2.35 Å, Caspase-7 in complex with Ac-ATS009-KE
1I4O 2.4 Å, Crystal structure of the xiap/caspase-7 complex

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