6R2W: Super-active FVIIa variant VYT

Crystal structure of the super-active FVIIa variant VYT in complex with tissue factor. Determined by X-ray diffraction at 1.25 Å resolution. Released 11 Dec 2019.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,757
Mol. weight: 70.02 kDa
Ligands: 0Z7, TMA, FUC, CA
Released: 11 Dec 2019

Explore 6R2W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R2W contains 29 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 H: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	5
β-strand	20-21	2	6
β-strand	30-35	6	7
β-strand	38-45	8	7
β-strand	50-53	4	7
α-helix	55-58	4
α-helix	64-66	3
β-strand	67-71	5	7
β-strand	75	1	8
β-strand	84-94	11	7
β-strand	107-111	5	7
α-helix	114-117	4
β-strand	118	1	9
β-strand	121	1	9
α-helix	123-124	2
β-strand	125	1	6
α-helix	129-134	6
α-helix	136-138	3
β-strand	141-146	6	6
β-strand	149	1	10
α-helix	155	1
β-strand	156	1	10
α-helix	157	1
β-strand	159	1	8
β-strand	161-168	8	6
α-helix	170-173	4
β-strand	185-188	4	6
β-strand	196	1	5
β-strand	205-210	6	6
β-strand	213-222	10	6
β-strand	233-237	5	6
α-helix	238-241	4
α-helix	242-250	9
α-helix	252-253	2
β-strand	258-261	4	7

Chain L: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	10-11	2
α-helix	13	1
α-helix	14-18	5
α-helix	24-31	8
α-helix	34-44	11
α-helix	49-52	4
β-strand	60-64	5	1
β-strand	67-71	5	1
α-helix	72-73	2
β-strand	76-77	2	2
β-strand	83-84	2	2
α-helix	94-97	4
β-strand	101-105	5	3
β-strand	108-113	6	3
β-strand	118-120	3	4
β-strand	127-129	3	4

Chain T: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	11
β-strand	20-26	7	11
α-helix	27-29	3
β-strand	32-40	9	12
β-strand	46-52	7	12
β-strand	56-58	3	11
α-helix	60-63	4
β-strand	71-79	9	12
β-strand	94-96	3	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	113-119	7	13
β-strand	122-127	6	13
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	202-207	6
β-strand	208-209	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor VII	L	protein	143	Homo sapiens	P08709 (AlphaFold model)
Coagulation factor VII	H	protein	249	Homo sapiens	P08709 (AlphaFold model)
Tissue factor	T	protein	210	Homo sapiens	P13726 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>6R2W_1 Coagulation factor VII (chains L)
ANAFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISYSDGDQCASSPCQNGGS
CKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSL
LADGVSCTPTVEYPCGKIPILEK

Sequence of entity 2 (H), FASTA

>6R2W_2 Coagulation factor VII (chains H)
IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHD
LSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERT
LAFVRFSLVSGWGQLLDRGATALELMVLNVPRVMTQDCEASYPGKITEYMFCAGYSDGSK
DSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRP
GVLLRAPFP

Sequence of entity 3 (T), FASTA

>6R2W_3 Tissue factor (chains T)
SGTTNTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLT
DEIVKDVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVG
TKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVD
KGENYCFSVQAVIPSRTVNRKSTDSPVECM

Ligands and cofactors

ID	Name	Formula	Copies
0Z7	N-acetyl-D-phenylalanyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-…	C27 H38 Cl N6 O4	1
TMA	Tetramethylammonium ion	C4 H12 N	10
FUC	alpha-L-fucopyranose	C6 H12 O5	1
CA	Calcium ion	Ca	9

Primary citation

Beating tissue factor at its own game: Design and properties of a soluble tissue factor-independent coagulation factor VIIa. Sorensen, A.B., Tuneew, I., Svensson, L.A. et al. J Biol Chem (2020) 295:517-528. DOI 10.1074/jbc.RA119.009183 · PubMed

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

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-[(…
4JZE 1.52 Å, Structure of factor VIIA in complex with the inhibitor 2-{2-[(1-aminoisoquinolin-6-yl)car…

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