7QOX: Plasma kallikrein heavy chain

Factor XI and Plasma Kallikrein apple domain structures reveals different kininogen bound complexes. Determined by X-ray diffraction at 2.32 Å resolution. Released 18 Jan 2023.

Method: X-ray diffraction
Resolution: 2.32 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,368
Mol. weight: 91.69 kDa
Ligands: PE4, NAG, PG6
Released: 18 Jan 2023

Explore 7QOX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QOX contains 28 α-helices and 41 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: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	1
β-strand	16-21	6	1
α-helix	25-34	10
β-strand	40-44	5	1
α-helix	46-48	3
α-helix	52-54	3
β-strand	57-61	5	1
β-strand	70-80	11	1
α-helix	86-88	3
β-strand	97-103	7	2
β-strand	105-111	7	2
α-helix	115-123	9
β-strand	130-134	5	2
α-helix	141-143	3
β-strand	146-151	6	2
α-helix	153-155	3
β-strand	159-170	12	2
α-helix	173-175	3
β-strand	186-191	6	3
β-strand	195-201	7	3
α-helix	205-214	10
β-strand	220-224	5	3
α-helix	231-233	3
β-strand	236-241	6	3
β-strand	251-260	10	3
α-helix	269-271	3
β-strand	278-283	6	4
β-strand	286-293	8	4
α-helix	296-305	10
β-strand	311-315	5	4
α-helix	318-320	3
β-strand	321-322	2	4
β-strand	325-332	8	4
β-strand	341-351	11	4

Chain B: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	5
β-strand	16-21	6	5
α-helix	25-34	10
β-strand	40-43	4	5
α-helix	46-48	3
α-helix	52-54	3
β-strand	57-61	5	5
β-strand	70-80	11	5
α-helix	86-88	3
β-strand	96-103	8	6
β-strand	105-111	7	6
α-helix	115-123	9
β-strand	130-134	5	6
α-helix	141-143	3
β-strand	146-151	6	6
α-helix	153-155	3
β-strand	159-170	12	6
α-helix	173-175	3
β-strand	186-191	6	7
β-strand	195-201	7	7
α-helix	205-214	10
β-strand	220-224	5	7
α-helix	231-233	3
β-strand	236-241	6	7
β-strand	251-260	10	7
α-helix	269-271	3
β-strand	278-284	7	8
β-strand	286-293	8	8
α-helix	296-305	10
β-strand	311-315	5	8
β-strand	326-332	7	8
β-strand	340-351	12	8

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	586-589	4

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	571-574	4
α-helix	586-590	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasma kallikrein heavy chain	A, B	protein	367	Homo sapiens	P03952 (AlphaFold model)
Kininogen-1 light chain	C, D	protein	29	Homo sapiens	P01042 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7QOX_1 Plasma kallikrein heavy chain (chains A, B)
RSHHHHHHGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFSFLPASSINDM
EKRFGCFLKDSVTGTLPKVHRTGAVSGHSLKQCGHQISACHRDIYKGVDMRGVNFNVSKV
SSVEECQKRCTNNIRCQFFSYATQTFHKAEYRNNCLLKYSPGGTPTAIKVLSNVESGFSL
KPCALSEIGCHMNIFQHLAFSDVDVARVLTPDAFVCRTICTYHPNCLFFTFYTNVWKIES
QRNVCLLKTSESGTPSSSTPQENTISGYSLLTCKRTLPEPCHSKIYPGVDFGGEELNVTF
VKGVNVCQETCTKMIRCQFFTYSLLPEDCKAEACKCFLRLSMDGSPTRIAYGTQGSSGYS
LRLCNTG

Sequence of entity 2 (C, D), FASTA

>7QOX_2 Kininogen-1 light chain (chains C, D)
TQSDDDWIPDIQIDPNGLSFNPISDFPDT

Ligands and cofactors

ID	Name	Formula	Copies
PE4	2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-etha…	C16 H34 O8	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
PG6	1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane	C12 H26 O6	1

Water and common crystallization additives (GOL, PG4, PEG) are not listed.

Primary citation

Plasma kallikrein structure reveals apple domain disc rotated conformation compared to factor XI. Li, C., Voos, K.M., Pathak, M. et al. J Thromb Haemost (2019) 17:759-770. DOI 10.1111/jth.14418 · PubMed

Other PDB entries of the same protein (UniProt P03952 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6I44 1.36 Å, Allosteric activation of human prekallikrein by apple domain disc rotation
2ANY 1.4 Å, Expression, Crystallization and the Three-dimensional Structure of the Catalytic Domain…
5TJX 1.41 Å, Structure of human plasma kallikrein
6T7P 1.42 Å, human plasmakallikrein protease domain in complex with active site directed inhibitor
5F8Z 1.5 Å, The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor…
5F8X 1.55 Å, The crystal structure of human plasma kallikrein in complex with its peptide inhibitor…
10LR 1.58 Å, N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy…
10MW 1.62 Å, N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy…
10MV 1.66 Å, N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy…
6O1S 1.7 Å, Structure of human plasma kallikrein protease domain with inhibitor
10QS 1.73 Å, N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy…
5F8T 1.75 Å, The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor…

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