3K2U: HGFA

Crystal structure of HGFA in complex with the allosteric inhibitory antibody Fab40. Determined by X-ray diffraction at 2.35 Å resolution. Released 15 Dec 2009.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,207
Mol. weight: 79.38 kDa
Released: 15 Dec 2009

Explore 3K2U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3K2U contains 23 α-helices and 65 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	40-48	9	3
β-strand	51-54	4	3
α-helix	56-59	4
α-helix	61-63	3
β-strand	64-68	5	3
β-strand	72	1	4
β-strand	81-83	3	3
β-strand	85-90	6	3
β-strand	104-108	5	3
α-helix	109-110	2
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-125	3
β-strand	135-140	6	2
β-strand	154	1	4
β-strand	156-162	7	2
α-helix	165-168	4
α-helix	173-175	3
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-203	6	2
β-strand	206-213	8	2
β-strand	226-230	5	2
α-helix	231-233	3
α-helix	235-241	7

Chain H: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	11-12	2	6
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	33-39	7	7
β-strand	45-52	8	7
β-strand	56-59	4	7
α-helix	61-63	3
β-strand	67-72	6	5
β-strand	77-82	6	5
α-helix	84-86	3
β-strand	88-95	8	7
β-strand	102-103	2	7
β-strand	107-109	3	7
β-strand	110-111	2	6
α-helix	114-116	3
β-strand	117	1	8
β-strand	120-124	5	9
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
β-strand	159	1	10
β-strand	164-165	2	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-185	10	9
α-helix	186-188	3
β-strand	189	1	11
β-strand	192	1	11
β-strand	195-200	6	10
α-helix	201-203	3
β-strand	205-210	6	10

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	14
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-124	3
β-strand	130-137	8	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	154	1	16
β-strand	159-163	5	15
β-strand	174-181	8	15
α-helix	183-186	4
β-strand	191-197	7	16
β-strand	205-210	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hepatocyte growth factor activator long chain	A	protein	257	Homo sapiens	Q04756 (AlphaFold model)
Hepatocyte growth factor activator short chain	B	protein	35	Homo sapiens	Q04756 (AlphaFold model)
Antibody, Fab fragment, Heavy Chain	H	protein	225	Homo sapiens
Antibody, Fab fragment, Light Chain	L	protein	214	Homo sapiens

Sequence of entity 1 (A), FASTA

>3K2U_1 Hepatocyte growth factor activator long chain (chains A)
IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFF
NRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGS
TFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYF
DCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIRP
PRRLVAPSAAAHHHHHH

Sequence of entity 2 (B), FASTA

>3K2U_2 Hepatocyte growth factor activator short chain (chains B)
VQLSPDLLATLPEPASPGRQACGRRHKKRTFLRPR

Sequence of entity 3 (H), FASTA

>3K2U_3 Antibody, Fab fragment, Heavy Chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFTINGTYIHWVRQAPGKGLEWVGGIYPAGGATYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAKWWAWPAFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 4 (L), FASTA

>3K2U_4 Antibody, Fab fragment, Light Chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSNRAPATFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Unraveling the allosteric mechanism of serine protease inhibition by an antibody. Ganesan, R., Eigenbrot, C., Wu, Y. et al. Structure (2009) 17:1614-1624. DOI 10.1016/j.str.2009.09.014 · PubMed

Other PDB entries of the same protein (UniProt Q04756 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2R0L 2.2 Å, Short Form HGFA with Inhibitory Fab75
1YC0 2.6 Å, short form HGFA with first Kunitz domain from HAI-1
1YBW 2.7 Å, Protease domain of HGFA with no inhibitor
2WUC 2.7 Å, Crystal structure of HGFA in complex with the allosteric non- inhibitory antibody…
2WUB 2.9 Å, Crystal structure of HGFA in complex with the allosteric non- inhibitory antibody…
2R0K 3.51 Å, Protease domain of HGFA with inhibitor Fab58

Browse structure collections

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