8QOD: Fviia

Crystal structure of fviia in complex with a benzamidine-based inhibitor. Determined by X-ray diffraction at 1.57 Å resolution. Released 9 Oct 2024.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,930
Mol. weight: 72.84 kDa
Ligands: CA, MG, WIZ, FUC
Released: 9 Oct 2024

Explore 8QOD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QOD contains 36 α-helices and 50 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	10-11	2
α-helix	13	1
α-helix	14-19	6
α-helix	24-31	8
α-helix	34-46	13
α-helix	49-52	4
β-strand	60-64	5	1
β-strand	67-71	5	1
β-strand	76-77	2	2
β-strand	83-84	2	2
α-helix	85-87	3
α-helix	94-97	4
β-strand	101-103	3	3
β-strand	111-113	3	3
β-strand	118-120	3	4
β-strand	127-129	3	4
α-helix	139-141	3

Chain B: 16 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	5
β-strand	20-21	2	6
α-helix	22-23	2
β-strand	30-35	6	7
β-strand	39-46	8	7
β-strand	51-54	4	7
α-helix	56-59	4
α-helix	61-63	3
β-strand	64-68	5	7
β-strand	72	1	8
β-strand	81-91	11	7
β-strand	104-108	5	7
α-helix	111-114	4
β-strand	115	1	9
β-strand	118	1	9
α-helix	120-121	2
β-strand	122	1	6
α-helix	123-125	3
α-helix	126-129B	6
α-helix	129D-129F	3
β-strand	135-140	6	6
β-strand	143	1	10
α-helix	150	1
β-strand	151	1	10
α-helix	152	1
β-strand	154	1	8
β-strand	156-163	8	6
α-helix	165-170A	7
α-helix	170C-170D	2
α-helix	170H-175	3
β-strand	180-183	4	6
β-strand	189	1	5
β-strand	198-203	6	6
β-strand	206-215	10	6
β-strand	226-230	5	6
α-helix	231-234	4
α-helix	235-242	8
α-helix	245-246	2
β-strand	251-254	4	7

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	11
β-strand	20-26	7	11
β-strand	32-40	9	12
α-helix	44-45	2
β-strand	46-52	7	12
β-strand	56-58	3	11
α-helix	60-63	4
β-strand	71-79	9	12
α-helix	91-92	2
β-strand	93-96	4	12
α-helix	97-99	3
β-strand	100	1	12
α-helix	102-105	4
β-strand	107	1	11
α-helix	108-111	4
β-strand	113-118	6	13
β-strand	122-127	6	13
α-helix	128-129	2
β-strand	131-136	6	14
β-strand	139-142	4	14
α-helix	143-147	5
α-helix	148-150	3
β-strand	152-159	8	15
β-strand	166-170	5	15
β-strand	174-178	5	13
β-strand	185-192	8	15
β-strand	201	1	15
α-helix	203-207	5
β-strand	208-209	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Factor VII light chain	A	protein	141	Homo sapiens	P08709 (AlphaFold model)
Coagulation factor VII	B	protein	254	Homo sapiens	P08709 (AlphaFold model)
Tissue factor	C	protein	243	Homo sapiens	P13726 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8QOD_1 Factor VII light chain (chains A)
AFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISYSDGDQCASSPCQNGGSCK
DQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLA
DGVSCTPTVEYPCGKIPILEK

Sequence of entity 2 (B), FASTA

>8QOD_2 Coagulation factor VII (chains B)
IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHD
LSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERT
LAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGY
SDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMR
SEPRPGVLLRAPFP

Sequence of entity 3 (C), FASTA

>8QOD_3 Tissue factor (chains C)
METPAWPRVPRPETAVARTLLLGWVFAQVAGASGTTNTVAAYNLTWKSTNFKTILEWEPK
PVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPAGNVESTGS
AGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFG
KDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVE
CMG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
MG	Magnesium ion	Mg	1
WIZ	3-[2-bromanyl-4-[(1~{S})-1-[[3-[(4-carbamimidoylphenyl)amino]-3-oxidanylidene-p…	C25 H23 Br N4 O5	1
FUC	alpha-L-fucopyranose	C6 H12 O5	1
GLC	alpha-D-glucopyranose	C6 H12 O6	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Crystallography and molecular simulations capture S1 pocket collapse in allosteric regulation of factor VIIa and other serine proteases. Tesmer, L., Hans Matter, H., Klingler, O. et al. To be published.

Other PDB entries of the same protein (UniProt P08709 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6R2W 1.25 Å, Crystal structure of the super-active FVIIa variant VYT in complex with tissue factor
5PAG 1.36 Å, Crystal Structure of Factor VIIa in complex with (2R)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-py…
5PAX 1.36 Å, Crystal Structure of Factor VIIa in complex with 1-(2,6-difluorophenyl)-3-[[3-[5-hydroxy-…
4YLQ 1.4 Å, Crystal Structure of a FVIIa-Trypsin Chimera (FT) in Complex with Soluble Tissue Factor
5PAO 1.4 Å, Crystal Structure of Factor VIIa in complex with (2S)-2,3-dihydroxy-N-[[3-[5-hydroxy-4-(1…
5PAV 1.4 Å, Crystal Structure of Factor VIIa in complex with N-(6-aminopyridin-3-yl)-5-hydroxy-1-phen…
5L0S 1.45 Å, human POGLUT1 in complex with Factor VII EGF1 and UDP
5PAE 1.45 Å, Crystal Structure of Factor VIIa in complex with (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-py…
5PB2 1.45 Å, Crystal Structure of Factor VIIa in complex with 2-phenyl-4-(1H-pyrrolo[3,2-c]pyridin-2-y…
5PAS 1.48 Å, Crystal Structure of Factor VIIa in complex with (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-py…
5PAC 1.5 Å, human factor VIIa in complex with 5-hydroxy-N-(4-oxo-3H-quinazolin-6-yl)-1-[3-[(phenylcar…
5PAF 1.5 Å, Crystal Structure of Factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-2-[3-[(…

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