6O5E: Vitronectin hemopexin-like domain

Crystal structure of the Vitronectin hemopexin-like domain. Determined by X-ray diffraction at 1.9 Å resolution. Released 18 Sept 2019.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,210
Mol. weight: 47.45 kDa
Released: 18 Sept 2019

Explore 6O5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O5E contains 16 α-helices and 39 β-strands across 2 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	159-161	3
β-strand	163-164	2	1
β-strand	168	1	1
β-strand	171-176	6	1
β-strand	179-184	6	1
β-strand	193-195	3	1
α-helix	196-200	5
β-strand	208-211	4	2
β-strand	219-223	5	2
β-strand	226-231	6	2
β-strand	234-235	2	2
α-helix	236	1
β-strand	241-242	2	2
α-helix	243-246	4
α-helix	250-251	2
β-strand	256-259	4	3
β-strand	270-275	6	3
β-strand	278-283	6	3
β-strand	333-334	2	3
α-helix	335-338	4
β-strand	340	1	4
β-strand	348-351	4	4
β-strand	435-440	6	4
β-strand	443-448	6	4
β-strand	453-454	2	4
α-helix	460	1
β-strand	463-464	2	4
α-helix	465-469	5

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	159-161	3
β-strand	163-166	4	5
β-strand	172-176	5	5
β-strand	179-183	5	5
β-strand	194-195	2	5
α-helix	196-199	4
β-strand	208-211	4	6
β-strand	218-223	6	6
β-strand	226-231	6	6
β-strand	234-235	2	6
α-helix	236	1
β-strand	241-242	2	6
α-helix	243-246	4
α-helix	250-251	2
β-strand	256-260	5	7
β-strand	270-275	6	7
β-strand	278-283	6	7
β-strand	333-334	2	7
α-helix	335-338	4
β-strand	340	1	8
β-strand	348-351	4	8
β-strand	435-440	6	8
β-strand	443-448	6	8
β-strand	453-454	2	8
α-helix	460	1
β-strand	463-464	2	8
α-helix	465-468	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitronectin	A, B	protein	204	Homo sapiens	P04004 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6O5E_1 Vitronectin (chains A, B)
MELCSGKPFDAFTDLKNGSLFAFRGQYSYELDEKAVRPGYPKLIRDVWGIEGPIDAAFTR
INSQGKTYLFKGSQYWRFEDGVLDPDYPRNISDGFDGIPDNVDAALALPAHSYSGRERVY
FFKGKQYWEYQFQRTSAGTRQPQFISRDWHGVPGQVDAAMAGRISVFFFSGDKYYRVNLR
TRRVDTVDPPYPRSIAQYWLGCPA

Primary citation

Structure of human Vitronectin C-terminal domain and interaction withYersinia pestisouter membrane protein Ail. Shin, K., Lechtenberg, B.C., Fujimoto, L.M. et al. Sci Adv (2019) 5:eaax5068-eaax5068. DOI 10.1126/sciadv.aax5068 · PubMed

Other PDB entries of the same protein (UniProt P04004 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RJ9 1.7 Å, Crystal structure of the Vitronectin hemopexin-like domain binding Calcium
1OC0 2.28 Å, plasminogen activator inhibitor-1 complex with somatomedin B domain of vitronectin
3BT2 2.5 Å, Structure of urokinase receptor, urokinase and vitronectin complex
3BT1 2.8 Å, Structure of urokinase receptor, urokinase and vitronectin complex
4K24 4.5 Å, Structure of anti-uPAR Fab ATN-658 in complex with uPAR
1S4G Somatomedin-B Domain of human plasma vitronectin.
1SSU Structural and biochemical evidence for disulfide bond heterogeneity in active forms of…
2JQ8 Solution structure of the Somatomedin B domain from vitronectin produced in Pichia…

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