2PUQ: Active site inhibited coagulation factor VIIA

Crystal structure of active site inhibited coagulation factor VIIA in complex with soluble tissue factor. Determined by X-ray diffraction at 2.05 Å resolution. Released 22 May 2007.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,306
Mol. weight: 62.58 kDa
Ligands: CA, FUC, BGC
Released: 22 May 2007

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

Secondary structure: helices and β-sheets

2PUQ contains 24 α-helices and 58 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 H: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	154	1	6
β-strand	157-158	2	7
α-helix	159-160	2
β-strand	167-172	6	8
β-strand	175-184	10	8
β-strand	187-190	4	8
α-helix	192-195	4
α-helix	201-203	3
β-strand	204-208	5	8
β-strand	212	1	9
β-strand	221-231	11	8
β-strand	244-248	5	8
β-strand	255	1	10
β-strand	258	1	10
α-helix	260-261	2
β-strand	262	1	7
α-helix	266-271	6
α-helix	273-275	3
β-strand	278-283	6	7
β-strand	286	1	11
α-helix	292	1
β-strand	293	1	11
α-helix	294	1
β-strand	296	1	9
β-strand	298-305	8	7
α-helix	307-313	7
α-helix	315-316	2
α-helix	320-322	3
β-strand	327-330	4	7
β-strand	338	1	6
β-strand	347-352	6	7
β-strand	355-364	10	7
β-strand	375-379	5	7
α-helix	380-383	4
α-helix	384-392	9
β-strand	400-403	4	8

Chain I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	7

Chain L: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	50-52	3
β-strand	60-61	2	1
β-strand	64	1	2
β-strand	67	1	2
β-strand	70-71	2	1
β-strand	76-77	2	3
β-strand	83-84	2	3
α-helix	85-87	3
α-helix	94-97	4
β-strand	101-105	5	4
β-strand	108-113	6	4
β-strand	118-120	3	5
β-strand	127-129	3	5

Chain T: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	12
β-strand	20-26	7	12
β-strand	32-40	9	13
α-helix	44-45	2
β-strand	46-52	7	13
β-strand	56-58	3	12
α-helix	60-63	4
β-strand	71-79	9	13
β-strand	93-96	4	13
α-helix	97-99	3
β-strand	100	1	13
α-helix	102-105	4
β-strand	107	1	12
α-helix	108-109	2
β-strand	113	1	14
β-strand	126	1	15
β-strand	127	1	14
β-strand	131-136	6	16
β-strand	139-142	4	16
α-helix	143-147	5
α-helix	148-150	3
β-strand	152-153	2	17
β-strand	156	1	18
β-strand	167	1	18
β-strand	170	1	17
β-strand	174	1	15
β-strand	187	1	19
β-strand	188	1	18
β-strand	191-192	2	17
β-strand	201	1	17
α-helix	204-207	4
β-strand	208	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor VII	L	protein	94	Homo sapiens	P08709 (AlphaFold model)
Coagulation factor VII	H	protein	254	Homo sapiens	P08709 (AlphaFold model)
Tissue factor	T	protein	204	Homo sapiens	P13726 (AlphaFold model)
Trp-tyr-thr-arg chloromethylketone inhibitor	I	protein	5

Sequence of entity 1 (L), FASTA

>2PUQ_1 Coagulation factor VII (chains L)
QCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGT
KRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILE

Sequence of entity 2 (H), FASTA

>2PUQ_2 Coagulation factor VII (chains H)
IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHD
LSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERT
LAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGY
SDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMR
SEPRPGVLLRAPFP

Sequence of entity 3 (T), FASTA

>2PUQ_3 Tissue factor (chains T)
TVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVK
DVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNV
TVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENY
CFSVQAVIPSRTVNRKSTDSPVEC

Sequence of entity 4 (I), FASTA

>2PUQ_4 TRP-TYR-THR-ARG CHLOROMETHYLKETONE INHIBITOR (chains I)
WYTRX

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
FUC	alpha-L-fucopyranose	C6 H12 O5	1
BGC	beta-D-glucopyranose	C6 H12 O6	1

Primary citation

Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa. Larsen, K.S., Ostergaard, H., Bjelke, J.R. et al. Biochem J (2007) 405:429-438. DOI 10.1042/BJ20061901 · PubMed

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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