3D6H: Caspase-1

Crystal structure of human caspase-1 with a naturally-occurring Asn263->Ser substitution in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK). Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Mar 2010.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,246
Mol. weight: 30.84 kDa
Released: 2 Mar 2010

Explore 3D6H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D6H contains 11 α-helices and 17 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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	133-135	3
α-helix	138-147	10
β-strand	152	1	1
β-strand	164-169	6	2
α-helix	182-195	14
α-helix	198	1
β-strand	199-204	6	2
α-helix	208-220	13
α-helix	222-226	5
β-strand	230-235	6	2
β-strand	238	1	3
β-strand	243-244	2	3
α-helix	245	1
β-strand	255-256	2	3
α-helix	258-264	7
α-helix	271-273	3
β-strand	278-283	6	2
β-strand	289	1	4

Chain B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	327-331	5	2
β-strand	337	1	4
β-strand	340	1	5
β-strand	341-342	2	6
β-strand	346-347	2	6
α-helix	348-360	13
α-helix	366-375	10
β-strand	388-390	3	2
β-strand	397	1	1

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Caspase-1	A	protein	179	Homo sapiens	P29466 (AlphaFold model)
Caspase-1 precursor	B	protein	89	Homo sapiens	P29466 (AlphaFold model)
N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide	C	protein	5

Sequence of entity 1 (A), FASTA

>3D6H_1 Caspase-1 (chains A)
MNPAMPTSSGSEGNVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPR
RTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHG
IREGICGKKHSEQVPDILQLNAIFSMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKD

Sequence of entity 2 (B), FASTA

>3D6H_2 Caspase-1 precursor (chains B)
MAIKKAHIEKDFIAFCSSTPDNVSWRHPTMGSVFIGRLIEHMQEYACSCDVEEIFRKVRF
SFEQPDGRAQMPTTERVTLTRCFYLFPGH

Sequence of entity 3 (C), FASTA

>3D6H_3 N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide (chains C)
XVADX

Primary citation

Mutated, structurally altered caspase-1 with decreased enzymatic and increased RIP2-meditated inflammatory activity leads to a new type of periodic fever (ICE fever). Rosen-Wolff, A., Romanowski, M.J., Ritter, L. et al. To be published (2008).

Other PDB entries of the same protein (UniProt P29466 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8WRA 1.45 Å, The Crystal Structure of CASP1 from Biortus
6BZ9 1.8 Å, Crystal structure of human caspase-1 in complex with Ac-FLTD-CMK
1SC3 1.8 Å, Crystal structure of the human caspase-1 C285A mutant in complex with malonate
2H54 1.8 Å, Crystal structure of human caspase-1 (Thr388->Ala) in complex with…
2HBQ 1.8 Å, Crystal structure of wildtype human caspase-1 in complex with…
3D6M 1.8 Å, Crystal structure of human caspase-1 with a naturally-occurring Lys319->Arg substitution…
6F6R 1.8 Å, Crystal structure of human Caspase-1 with N-{3-[1-((S)-2-Hydroxy-5-oxo-tetrahydro-furan-3…
1RWX 1.85 Å, Crystal structure of human caspase-1 in complex with 4-oxo-3-{6-[4-(quinoxalin-2-yloxy)-b…
2H4Y 1.9 Å, Crystal structure of human caspase-1 (Arg286->Lys) in complex with…
2HBZ 1.9 Å, Crystal structure of human caspase-1 (Arg286->Ala, Glu390->Ala) in complex with…
3D6F 1.9 Å, Crystal structure of human caspase-1 with a naturally-occurring Arg240->Gln substitution…
6PZP 1.94 Å, Crystal structure of caspase-1 in complex with VX-765

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