5NMV: 2F22 Fab fragment against TFPI1

Crystal structure of 2F22 Fab fragment against TFPI1. Determined by X-ray diffraction at 1.65 Å resolution. Released 28 Mar 2018.

Method: X-ray diffraction
Resolution: 1.65 Å
Organisms: Mus, Homo sapiens
Chains: 3
Atoms: 4,403
Mol. weight: 57.22 kDa
Released: 28 Mar 2018

Explore 5NMV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NMV contains 22 α-helices and 48 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: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	34-40	7	8
β-strand	44-51	8	8
β-strand	57-59	3	8
α-helix	64-66	3
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	87-89	3
β-strand	91-98	8	8
β-strand	108-111	4	8
β-strand	115-117	3	8
β-strand	118-119	2	7
α-helix	122-124	3
β-strand	125	1	9
α-helix	126-127	2
β-strand	128-132	5	10
β-strand	143-153	11	10
β-strand	154	1	9
β-strand	159-162	4	11
α-helix	163-165	3
β-strand	167	1	11
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-178	2	10
β-strand	184-193	10	10
α-helix	194-196	3
β-strand	203-208	6	11
α-helix	209-211	3
β-strand	213-218	6	11

Chain K: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
α-helix	23-27	5
α-helix	29-30	2
β-strand	39-45	7	12
β-strand	50-56	7	12
β-strand	59	1	8
β-strand	66	1	12
α-helix	69-76	8

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-5	2	1
β-strand	10-13	4	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	85-91	7	2
β-strand	95-97	3	2
β-strand	101-105	5	2
β-strand	110	1	3
α-helix	111-112	2
β-strand	113-117	5	4
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	4
β-strand	139	1	3
β-strand	144-149	6	5
β-strand	152-153	2	5
α-helix	154	1
β-strand	158-162	5	4
α-helix	163-166	4
β-strand	172-181	10	4
α-helix	182-185	4
β-strand	190-196	7	5
β-strand	204-209	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab light chain	L	protein	213	Mus
Fab heavy chain	H	protein	222	Mus
Tissue factor pathway inhibitor	K	protein	86	Homo sapiens	P10646 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>5NMV_1 Fab light chain (chains L)
GIVMTQSQKFMSTTVGDRVSITCKASQSVGPAVAWYQQKPGQSPKLLIYSASNRYTGVPD
RFTGSGSGADFTLTISNLHSEDLADYFCQQYTSYPTFGGGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>5NMV_2 Fab heavy chain (chains H)
QVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLAVIWRGGSIDYN
AAFMSRLSITKDNSKSQVFFKMNSLQADDTAIYYCAKNSHGNYVGYAMDYWGQGTSVTVS
SASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESK

Sequence of entity 3 (K), FASTA

>5NMV_3 Tissue factor pathway inhibitor (chains K)
GSSGSSGDSEEDEEHTIITDTELPPLKLMHSFCAFKADDGPCKAIMKRFFFNIFTRQCEE
FIYGGCEGNQNRFESLEECKKMCTRD

Primary citation

Factor Xa and VIIa inhibition by tissue factor pathway inhibitor is prevented by a monoclonal antibody to its Kunitz-1 domain. Augustsson, C., Svensson, A., Kjaer, B. et al. J Thromb Haemost (2018) 16:893-904. DOI 10.1111/jth.14000 · PubMed

Other PDB entries of the same protein (UniProt P10646 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4DTG 1.8 Å, Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa…
6BX8 1.98 Å, Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant…
4BQD 2.48 Å, KD1 of human TFPI in complex with a synthetic peptide
1TFX 2.6 Å, Complex of the second kunitz domain of tissue factor pathway inhibitor with porcine…
7V1N 3.2 Å, Structure of the Clade 2 C. difficile TcdB in complex with its receptor TFPI
9P0X 3.7 Å, Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted)
1ADZ The solution structure of the second kunitz domain of tissue factor pathway inhibitor,…
1IRH The Solution Structure of The Third Kunitz Domain of Tissue Factor Pathway Inhibitor

Browse structure collections

About this viewer

MolViewer shows 5NMV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.