Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Complex of human neutrophil elastase with 1/2SLPI.

(2008) J Synchrotron Radiat 15

PubMed: 18421166 | PubMedCentral: PMC2394824 | DOI: 10.1107/S0909049507060670

The main-chain trace of HNE shows no differences from PDB (Protein Data Bank) id 1B0F (Cregge et al. , 1998 ▶ ).

Publication Year: 2008

An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues.

(2012) PLoS One 7

PubMed: 22811760 | PubMedCentral: PMC3394801 | DOI: 10.1371/journal.pone.0040408

The distances are specified in the reference protein (PDBid:1B0F) in A. For the remaining, we show the deviation from the reference value.

g002 Figure 2 Superimposition of pseudechetoxin (PDB id: 1CFE, in green) and P14a (PDB id: 1B0F, in blue) and using TopMatch.

( b ) Human neutrophil elastase (PDBid:1B0F) with active site atoms - Ser195/OG, His57/ND1, Ser214/OG, Gly193/N.

Atom Before After Coordinates X Y Z X Y Z PDB: 1B0F (template) Ser195/OG 64.4 57 53.8 0 0 0 His57/ND1 63.3 54.8 58.2 5 0 0 Ser214/OG 63.6 50.6 56.1 5 4.7 0 PDB: 1CFE(target) Ser49/OG 8.8 −6.3 −4.8 0 0 0 His48/ND1 9.2 −2.4 −1.8 4.9 0 0 Tyr36/OH 13.7 −1.6 −3.7 4.7 5 0 After applying linear and rotational transformations on both proteins, Ser195 and Ser49 lie at the center of the coordinate axis, His57 and His48 lie on the -X-Y axis (Y = 0) and Ser214 and Tyr36 lie on the X–Y plane (Z = 0).

g003 Figure 3 Superimposing proteins based on partial matches (Ser195, His57, Ser214 from PDBid:1B0F) and (Ser49, His48, Tyr36 from PDBid:1CFE).

It can be seen that the Asp102 in PDBid:1B0F is close to Asn35 and Ser39 in PDBid:1CFE.

1 Selecting the Best Candidate We chose the HNE protein with PDBid:1B0F as the template protein.

Ser195 from PDBid:1B0F and Ser49 from PDBid:1CFE coincide and is colored in black.

a b c d 1B0F Motif SER195 HIS57 SER214 GLY193 1CFE motif SER49 HIS48 TYR36 ALA51 ab ac ad bc bd cd PDB Pairwise Distances 1B0F 5 6.8 4.6 4.7 9.4 11 1CFE 4.9 6.8 4.5 5 9.1 10 Pairwise Potential difference 1B0F 53.7 105.7 −111.1 51.9 −164.9 −216.8 1CFE 15.3 88.6 −58.1 73.3 −73.4 −146.8 Spatial and electrostatic potential difference (PD) congruence in cognate pairs in the human neutrophil elastase (PDBid:1B0F) and the pathogenesis related P14A protein (PDBid:1CFE) for an extended set of four residues in the active site.

Predicted residues Pairwise Distances in Å Pairwise Potential difference PDB: a b c ab ac bc ab ac bc Score 1B0F Ser195 His57 Ser214 5 6.8 4.7 53.7 105.7 51.9 0 1CFE (Ser214 can be Ser only) Ser49 His48 Ser120 0.1 −0.2 1.9 15.3 83.9 68.6 0.111 1CFE (Ser214 can be Ser or Tyr) Ser49 His48 Tyr36 0.1 0.3 −0.3 15.3 88.6 73.3 0.023 When the position Ser214 in the input motif (Ser195, His57, Ser214) can be matched by a Ser or Tyr, Tyr36 has a much better spatial orientation with respect to Ser49 and His48 as compared to Ser120 in the P14A protein (PDBid:1CFE).

( a ) Superimposition of both proteins: Human neutrophilelastase (PDBid:1B0F) is in grey, and P14A (PDBid:1CFE) is in green.

t004 Table 4 Superimposing proteins based on partial matches (Ser195, His57, Ser214 from PDBid:1B0F) and (Ser49, His48, Tyr36 from PDBid:1CFE).

Table 4 shows the coordinates of the atoms before and after the transformations when the partial match - (Ser195/OG, His57/ND1, Ser214/OG, Gly193/N - PDBid:1B0F) and (Ser49/OG, His48/ND1, Tyr36/OH, Ala51/N - PDBid:1CFE) - are superimposed.

Publication Year: 2012

Inhibition of human neutrophil elastase by pentacyclic triterpenes.

(2013) PLoS One 8

PubMed: 24376583 | PubMedCentral: PMC3869726 | DOI: 10.1371/journal.pone.0082794

Molecular Docking The crystal structure (PDB ID: 1B0F) of HNE in complex with the inhibitor SEI was downloaded from the RCSB protein data bank [22] .

The root mean square deviation between the conformational superposition of SEI from 1B0F crystal structure and that from the docking result was 0.44 Å, which suggests that the parameter set for the AutoDock simulation was reasonable for reproducing the X-ray structure.

Publication Year: 2013