2WUB: HGFA

Crystal structure of HGFA in complex with the allosteric non- inhibitory antibody Fab40.deltaTrp. Determined by X-ray diffraction at 2.9 Å resolution. Released 15 Dec 2009.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: HOMO SAPIENS
Chains: 8
Atoms: 10,198
Mol. weight: 158.71 kDa
Released: 15 Dec 2009

Explore 2WUB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2WUB contains 45 α-helices and 122 β-strands across 6 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	1
β-strand	30-35	6	2
β-strand	40-48	9	2
β-strand	51-54	4	2
α-helix	56-58	3
α-helix	61-63	3
β-strand	64-68	5	2
β-strand	72	1	3
β-strand	81-90	10	2
β-strand	104-108	5	2
α-helix	109-110	2
α-helix	120-121	2
β-strand	122	1	1
α-helix	123	1
β-strand	135-140	6	1
β-strand	143	1	4
β-strand	151	1	4
β-strand	154	1	3
β-strand	156-163	8	1
α-helix	164	1
α-helix	165-168	4
β-strand	180-183	4	1
β-strand	198-203	6	1
β-strand	206-213	8	1
β-strand	226-229	4	1
α-helix	231-234	4
α-helix	235-242	8

Chain C: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	5
β-strand	30-35	6	6
β-strand	40-48	9	6
β-strand	51-54	4	6
α-helix	56-58	3
α-helix	61-63	3
β-strand	64-68	5	6
β-strand	72	1	7
β-strand	81-90	10	6
β-strand	104-108	5	6
α-helix	109-110	2
α-helix	120-121	2
β-strand	122	1	5
α-helix	123-125	3
β-strand	135-140	6	5
β-strand	154	1	7
β-strand	156-162	7	5
α-helix	165-168	4
β-strand	180-183	4	5
β-strand	198-203	6	5
β-strand	206-213	8	5
β-strand	226-230	5	5
α-helix	231-234	4
α-helix	235-242	8

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-52	8	10
α-helix	52A-54	3
β-strand	56-59	4	10
α-helix	61-63	3
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-94	7	10
β-strand	95	1	11
β-strand	100	1	11
β-strand	107-109	3	10
β-strand	110-111	2	9
β-strand	117	1	12
α-helix	118-119	2
β-strand	120-124	5	13
β-strand	136-145	10	13
β-strand	146	1	12
β-strand	151-154	4	14
α-helix	155-157	3
β-strand	159	1	14
β-strand	163-165	3	13
α-helix	166-168	3
β-strand	176-184	9	13
α-helix	186-189	4
β-strand	194-200	7	14
α-helix	201-203	3
β-strand	205-211	7	14

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-13	4	16
β-strand	19-25	7	15
β-strand	33-38	6	16
β-strand	45-49	5	16
β-strand	53-54	2	16
α-helix	55	1
β-strand	62-66	5	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	85-90	6	16
α-helix	96	1
β-strand	97-98	2	16
β-strand	102-106	5	16
α-helix	107	1
β-strand	111	1	17
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	18
β-strand	140	1	17
β-strand	145-150	6	19
β-strand	154	1	19
β-strand	159-163	5	18
β-strand	173-182	10	18
α-helix	183-187	5
β-strand	191-197	7	19
β-strand	205-210	6	19

Chain Q: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
β-strand	10-13	4	21
β-strand	19-25	7	20
β-strand	33-38	6	21
β-strand	45-49	5	21
β-strand	53-54	2	21
β-strand	62-66	5	20
β-strand	70-75	6	20
α-helix	80-82	3
β-strand	85-90	6	21
α-helix	96	1
β-strand	97-98	2	21
β-strand	102-106	5	21
β-strand	111	1	22
β-strand	114-118	5	23
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	23
β-strand	140	1	22
β-strand	145-150	6	24
β-strand	154	1	24
β-strand	159-163	5	23
β-strand	173-182	10	23
α-helix	183-187	5
β-strand	191-197	7	24
β-strand	205-210	6	24

Chain R: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	25
β-strand	11-12	2	26
β-strand	18-25	8	25
β-strand	33-39	7	21
β-strand	45-52	8	21
β-strand	56-59	4	21
α-helix	61-63	3
β-strand	67-72	6	25
β-strand	77-82	6	25
α-helix	84-86	3
β-strand	88-98	10	21
β-strand	100A-103	5	21
β-strand	107-109	3	21
β-strand	110-111	2	26
β-strand	117	1	27
β-strand	120-123	4	28
β-strand	136-145	10	28
β-strand	146	1	27
β-strand	151-154	4	29
α-helix	155-157	3
β-strand	159	1	29
β-strand	163-165	3	28
α-helix	166-168	3
β-strand	176-184	9	28
α-helix	187-189	3
β-strand	196-199	4	29
β-strand	200	1	30
α-helix	201-203	3
β-strand	205	1	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hepatocyte growth factor activator long chain	A, C	protein	257	HOMO SAPIENS	Q04756 (AlphaFold model)
Hepatocyte growth factor activator short chain	B, D	protein	35	HOMO SAPIENS	Q04756 (AlphaFold model)
FAB fragment FAB40.DELTATRP heavy chain	H, R	protein	224	HOMO SAPIENS
FAB fragment FAB40.DELTATRP light chain	L, Q	protein	214	HOMO SAPIENS

Sequence of entity 1 (A, C), FASTA

>2WUB_1 HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN (chains A, C)
IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFF
NRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGS
TFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYF
DCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIRP
PRRLVAPSAAAHHHHHH

Sequence of entity 2 (B, D), FASTA

>2WUB_2 HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN (chains B, D)
VQLSPDLLATLPEPASPGRQACGRRHKKRTFLRPR

Sequence of entity 3 (H, R), FASTA

>2WUB_3 FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN (chains H, R)
EVQLVESGGGLVQPGGSLRLSCAASGFTINGTYIHWVRQAPGKGLEWVGGIYPAGGATYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAKWAWPAFDYWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 4 (L, Q), FASTA

>2WUB_4 FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN (chains L, Q)
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. 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
3K2U 2.35 Å, Crystal structure of HGFA in complex with the allosteric inhibitory antibody Fab40
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…
2R0K 3.51 Å, Protease domain of HGFA with inhibitor Fab58

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