6GWP: Plasminogen Activator Inhibitor-1

Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64). Determined by X-ray diffraction at 2.28 Å resolution. Released 1 Jan 2020.

Method: X-ray diffraction
Resolution: 2.28 Å
Organisms: Homo sapiens, Vicugna pacos
Chains: 3
Atoms: 4,750
Mol. weight: 68.59 kDa
Released: 1 Jan 2020

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

Secondary structure: helices and β-sheets

6GWP contains 25 α-helices and 38 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 A: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
β-strand	32-34	3	1
α-helix	36-49	14
α-helix	52-62	11
α-helix	72-83	12
β-strand	91-100	10	2
α-helix	103-106	4
α-helix	109-117	9
α-helix	120-121	2
β-strand	122-124	3	2
α-helix	129-143	15
α-helix	149-151	3
α-helix	153-156	4
β-strand	163-171	9	2
α-helix	173-174	2
β-strand	175	1	3
α-helix	178-180	3
α-helix	181-183	3
β-strand	185-190	6	1
β-strand	196-214	19	1
β-strand	220-227	8	1
β-strand	228	1	3
β-strand	233-240	8	1
α-helix	248-251	4
α-helix	256-264	9
β-strand	267-276	10	1
β-strand	278-285	8	2
α-helix	287-292	6
α-helix	297-299	3
β-strand	319-328	10	2
α-helix	342-345	4
α-helix	348-349	2
β-strand	350-353	4	1
β-strand	358-364	7	1
β-strand	369-376	8	1

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-12	3	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	33-39	7	5
α-helix	44-45	2
β-strand	46-51	6	5
β-strand	58-60	3	5
β-strand	68-73	6	4
α-helix	74-76	3
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-100	9	5
β-strand	103-106	4	5
β-strand	110-114	5	5

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
β-strand	33-39	7	7
β-strand	46-51	6	7
β-strand	58-60	3	7
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-99	8	7
α-helix	108	1
β-strand	110-111	2	7
β-strand	115-119	5	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasminogen Activator Inhibitor-1	A	protein	379	Homo sapiens	P05121 (AlphaFold model)
VHH-2g-42	B	protein	116	Vicugna pacos
VHH-2w-64	C	protein	121	Vicugna pacos

Sequence of entity 1 (A), FASTA

>6GWP_1 Plasminogen Activator Inhibitor-1 (chains A)
VHHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQA
AMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRST
VKQVDFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFP
DSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAP
YEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFR
PFQADFTSLSDQEPLHVALALQKVKIEVNESGTVASSSTAVIVSARMAPEEIIIDRPFLF
VVRHNPTGTVLFMGQVMEP

Sequence of entity 2 (B), FASTA

>6GWP_2 VHH-2g-42 (chains B)
QVQLVESGGGLVQPGGRLRLSCAASGFTFRTYAMQWYRQSPGTERELVAAISNIGGVTDY
GDSVKGRFTISRDNAKTTVYLEMNSLKPEDTATYYCSAVRLPQRYWGRGTQVTVSS

Sequence of entity 3 (C), FASTA

>6GWP_3 VHH-2w-64 (chains C)
QVQLVESGGGLVQAGGSLRLSCAASGFTFDDYSIAWFRQAPGKEREGVSCISSSDGSAYY
ADSVKGRFTISSDNAKNTVYLQMNSLKPEDTAVYYCAAVWARVCRNPYDYWGQGTQVTVS
S

Primary citation

Molecular mechanism of two nanobodies that inhibit PAI-1 activity reveals a modulation at distinct stages of the PAI-1/plasminogen activator interaction. Sillen, M., Weeks, S.D., Zhou, X. et al. J Thromb Haemost (2020) 18:681-692. DOI 10.1111/jth.14716 · PubMed

Other PDB entries of the same protein (UniProt P05121 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AQF 1.77 Å, Crystal Structure of Small Molecule Inhibitor TM5484 Bound to Stabilized Active…
1LJ5 1.8 Å, 1.8A Resolution Structure of Latent Plasminogen Activator Inhibitor-1(PAI-1)
6ZRV 1.88 Å, Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F)…
1A7C 1.95 Å, Human plasminogen activator inhibitor type-1 in complex with a pentapeptide
3CVM 2.02 Å, High resolution structure of a stable Plasminogen activator inhibitor type-1 in its…
6GWN 2.03 Å, Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F)…
1DVN 2.1 Å, Latent form of plasminogen activator inhibitor-1 (pai-1)
4G8R 2.19 Å, Crystal Structure of a novel small molecule inactivator bound to plasminogen activator…
7AQG 2.27 Å, Crystal Structure of Small Molecule Inhibitor TM5484 Bound to Stabilized Active…
1OC0 2.28 Å, plasminogen activator inhibitor-1 complex with somatomedin B domain of vitronectin
3PB1 2.3 Å, Crystal Structure of a Michaelis Complex between Plasminogen Activator Inhibitor-1 and…
3Q02 2.3 Å, Crystal structure of plasminogen activator inhibitor-1 in a metastable active…

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