4IBL: Rubidium Sites in Blood Coagulation Factor VIIa

Rubidium Sites in Blood Coagulation Factor VIIa. Determined by X-ray diffraction at 1.8 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,267
Mol. weight: 71.77 kDa
Ligands: BGC, BEN, RB, CA
Released: 16 Apr 2014

Explore 4IBL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IBL 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 H: 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	165-170	6
α-helix	170H-175	3
β-strand	180-183	4	6
β-strand	189	1	5
α-helix	192-194	3
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 L: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	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
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	101-105	5	3
β-strand	108-113	6	3
β-strand	118-120	3	4
β-strand	127-129	3	4
α-helix	139-141	3

Chain T: 11 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
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	113-119	7	13
β-strand	122-127	6	13
α-helix	128-130	3
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
Coagulation factor VII	L	protein	152	Homo sapiens	P08709 (AlphaFold model)
Coagulation factor VII	H	protein	254	Homo sapiens	P08709 (AlphaFold model)
Tissue factor	T	protein	219	Homo sapiens	P13726 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>4IBL_1 Coagulation factor VII (chains L)
ANAFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISYSDGDQCASSPCQNGGS
CKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSL
LADGVSCTPTVEYPCGKIPILEKRNASKPQGR

Sequence of entity 2 (H), FASTA

>4IBL_2 Coagulation factor VII (chains H)
IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHD
LSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERT
LAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGY
SDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMR
SEPRPGVLLRAPFP

Sequence of entity 3 (T), FASTA

>4IBL_3 Tissue factor (chains T)
SGTTNTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLT
DEIVKDVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVG
TKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVD
KGENYCFSVQAVIPSRTVNRKSTDSPVECMGQEKGEFRE

Ligands and cofactors

ID	Name	Formula	Copies
BGC	beta-D-glucopyranose	C6 H12 O6	1
BEN	Benzamidine	C7 H8 N2	1
RB	Rubidium ion	Rb	6
CA	Calcium ion	Ca	4
MG	Magnesium ion	Mg	3
FUC	alpha-L-fucopyranose	C6 H12 O5	1

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

Primary citation

Structure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidium. Vadivel, K., Schmidt, A., Cascio, D. et al. Acta Crystallogr D Biol Crystallogr (2021) D77:809-819. DOI 10.1107/S2059798321003922

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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