1JPS: Tissue factor

Crystal structure of tissue factor in complex with humanized Fab D3h44. Determined by X-ray diffraction at 1.85 Å resolution. Released 3 Feb 2002.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,437
Mol. weight: 72.39 kDa
Released: 3 Feb 2002

Explore 1JPS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1JPS contains 21 α-helices and 66 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: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-52	8	8
β-strand	57-60	4	8
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-99	8	8
β-strand	104-107	4	8
β-strand	111-115	5	8
β-strand	121	1	9
β-strand	124-128	5	10
β-strand	139-149	11	10
β-strand	150	1	9
β-strand	155-158	4	11
α-helix	159-161	3
β-strand	163	1	11
β-strand	167-169	3	10
α-helix	170-172	3
β-strand	173-174	2	10
β-strand	180-189	10	10
α-helix	190-192	3
β-strand	193	1	12
β-strand	196	1	12
β-strand	199-204	6	11
α-helix	205-207	3
β-strand	209-214	6	11

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	93	1	3
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	4
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
α-helix	155	1
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-186	4
β-strand	191-197	7	6
β-strand	205-210	6	6

Chain T: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	13
β-strand	20-26	7	13
β-strand	32-39	8	14
β-strand	46-52	7	14
β-strand	56-58	3	13
α-helix	60-63	4
β-strand	71	1	15
β-strand	72-79	8	14
β-strand	93-96	4	14
β-strand	100	1	15
α-helix	102-105	4
β-strand	107	1	13
α-helix	108-111	4
β-strand	113-119	7	16
β-strand	122-127	6	16
α-helix	128-130	3
β-strand	131-135	5	17
β-strand	140-142	3	17
α-helix	143-147	5
α-helix	148-150	3
β-strand	152-159	8	3
β-strand	166-170	5	3
β-strand	174-178	5	16
β-strand	185-192	8	3
β-strand	201	1	3
α-helix	203-207	5
β-strand	208-209	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
immunoglobulin Fab D3H44, light chain	L	protein	214	Homo sapiens
immunoglobulin Fab D3H44, heavy chain	H	protein	225	Homo sapiens
tissue factor	T	protein	219	Homo sapiens	P13726 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1JPS_1 immunoglobulin Fab D3H44, light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASRDIKSYLNWYQQKPGKAPKVLIYYATSLAEGVPS
RFSGSGSGTDYTLTISSLQPEDFATYYCLQHGESPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>1JPS_2 immunoglobulin Fab D3H44, heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKEYYMHWVRQAPGKGLEWVGLIDPEQGNTIY
DPKFQDRATISADNSKNTAYLQMNSLRAEDTAVYYCARDTAAYFDYWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (T), FASTA

>1JPS_3 tissue factor (chains T)
SGTTNTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLT
DEIVKDVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVG
TKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVD
KGENYCFSVQAVIPSRTVNRKSTDSPVECMGQEKGEFRE

Primary citation

The 1.85 A resolution crystal structures of tissue factor in complex with humanized Fab D3h44 and of free humanized Fab D3h44: revisiting the solvation of antigen combining sites. Faelber, K., Kirchhofer, D., Presta, L. et al. J Mol Biol (2001) 313:83-97. DOI 10.1006/jmbi.2001.5036 · PubMed

Other PDB entries of the same protein (UniProt P13726 (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
4YLQ 1.4 Å, Crystal Structure of a FVIIa-Trypsin Chimera (FT) in Complex with Soluble Tissue Factor
8QOD 1.57 Å, Crystal structure of fviia in complex with a benzamidine-based inhibitor
2HFT 1.69 Å, The crystal structure of the extracellular domain of human tissue factor at 1.7 Å…
2C4F 1.72 Å, crystal structure of factor VII.stf complexed with pd0297121
3TH2 1.72 Å, Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of…
2A2Q 1.8 Å, Complex of Active-site Inhibited Human Coagulation Factor VIIa with Human Soluble Tissue…
3TH4 1.8 Å, Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of…
4IBL 1.8 Å, Rubidium Sites in Blood Coagulation Factor VIIa
2AER 1.87 Å, Crystal Structure of Benzamidine-Factor VIIa/Soluble Tissue Factor complex.
8QQ6 1.87 Å, Crystal structure of fviia in complex with a benzamidine-based inhibitor
2FLB 1.95 Å, Discovery of a Novel Hydroxy Pyrazole Based Factor IXa Inhibitor

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