3UT3: Plasminogen activator inhibitor 1

A novel PAI-I inhibitor and its structural mechanism. Determined by X-ray diffraction at 2.42 Å resolution. Released 6 Feb 2013.

Method: X-ray diffraction
Resolution: 2.42 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,638
Mol. weight: 169.53 kDa
Ligands: EMJ
Released: 6 Feb 2013

Explore 3UT3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3UT3 contains 59 α-helices and 66 β-strands across 4 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: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	8-26	19
β-strand	32-34	3	1
α-helix	36-48	13
α-helix	52-62	11
α-helix	71-82	12
β-strand	91-92	2	2
β-strand	95-100	6	2
α-helix	109-117	9
β-strand	122-124	3	2
α-helix	126-128	3
α-helix	130-143	14
α-helix	152-156	5
β-strand	163-171	9	2
α-helix	173-174	2
β-strand	175	1	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
α-helix	229-231	3
β-strand	233-240	8	1
α-helix	248-251	4
α-helix	256-265	10
β-strand	267-276	10	1
β-strand	278-285	8	2
α-helix	287-291	5
α-helix	297-299	3
β-strand	319-328	10	2
β-strand	342-346	5	4
β-strand	350-353	4	1
β-strand	358-364	7	1
β-strand	369-376	8	1

Chain B: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-25	20
β-strand	32-34	3	5
α-helix	36-48	13
α-helix	52-62	11
α-helix	71-82	12
β-strand	91-100	10	6
α-helix	105-106	2
α-helix	109-117	9
β-strand	122-124	3	6
α-helix	129-142	14
α-helix	152-156	5
β-strand	163-172	10	6
β-strand	175	1	7
α-helix	178-180	3
α-helix	181-183	3
β-strand	185-190	6	5
β-strand	196-214	19	5
β-strand	220-227	8	5
β-strand	228	1	7
β-strand	233-240	8	5
α-helix	248-251	4
α-helix	256-264	9
β-strand	267-276	10	5
β-strand	278-285	8	6
α-helix	287-291	5
α-helix	297-299	3
β-strand	319-328	10	6
β-strand	351-353	3	5
β-strand	358-364	7	5
β-strand	369-376	8	5

Chain C: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
β-strand	32-34	3	8
α-helix	36-48	13
α-helix	52-62	11
α-helix	71-82	12
β-strand	91-100	10	4
α-helix	105-106	2
α-helix	109-117	9
α-helix	121	1
β-strand	122-124	3	4
α-helix	129-143	15
α-helix	152-156	5
β-strand	163-171	9	4
α-helix	173-174	2
β-strand	175	1	9
α-helix	178-180	3
α-helix	181-183	3
β-strand	185-190	6	8
β-strand	196-214	19	8
β-strand	220-227	8	8
β-strand	228	1	9
α-helix	229-231	3
β-strand	233-240	8	8
α-helix	248-251	4
α-helix	256-264	9
β-strand	267-276	10	8
β-strand	278-285	8	4
α-helix	287-291	5
α-helix	297-299	3
β-strand	319-328	10	4
β-strand	350-353	4	8
β-strand	358-364	7	8
β-strand	369-376	8	8

Chain D: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
β-strand	32-34	3	10
α-helix	36-47	12
α-helix	52-62	11
α-helix	71-81	11
β-strand	91-100	10	11
α-helix	104-106	3
α-helix	109-117	9
β-strand	122-124	3	11
α-helix	129-142	14
α-helix	152-156	5
β-strand	163-172	10	11
β-strand	175	1	12
α-helix	178-180	3
α-helix	181-183	3
β-strand	185-190	6	10
β-strand	196-214	19	10
β-strand	220-227	8	10
β-strand	228	1	12
β-strand	233-240	8	10
α-helix	248-251	4
α-helix	256-264	9
β-strand	267-276	10	10
β-strand	278-285	8	11
α-helix	287-291	5
β-strand	319-328	10	11
β-strand	351-353	3	10
β-strand	358-364	7	10
β-strand	369-376	8	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Plasminogen activator inhibitor 1	A, B, C, D	protein	375	Homo sapiens	P05121 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3UT3_1 Plasminogen activator inhibitor 1 (chains A, B, C, D)
PSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGF
KIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQV
DFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSST
HRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKE
VPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQA
DFTSLSDQEPLHVALALQKVKIEVNESGTVASSSTAVIVSARMAPEEIIIDRPFLFVVRH
NPTGTVLFMGQVMEP

Ligands and cofactors

ID	Name	Formula	Copies
EMJ	2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione	C17 H26 O4	1

Primary citation

A novel PAI-I inhibitor and its structural mechanism. Lin, Z.H., Hong, Z.B., Shi, X.L. et al. To be published.

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
6GWP 2.28 Å, Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in…
3PB1 2.3 Å, Crystal Structure of a Michaelis Complex between Plasminogen Activator Inhibitor-1 and…

Browse structure collections

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