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PDB ID Mentions in PubMed Central Article count: 5

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Exploiting protein flexibility to predict the location of allosteric sites.

(2012) BMC Bioinformatics 13

PubMed: 23095452 | PubMedCentral: PMC3562710 | DOI: 10.1186/1471-2105-13-273

To further explore this idea, we analyzed the human LDH homolog ([PDB:1I10]) as well, which shows a sequence identity of 37.7% and a local RMSD of 1.04 Å according to the SUPERPOSE web server ... 57 ] when compared to Bifidobacterium longum LDH.

Publication Year: 2012

Human lactate dehydrogenase a inhibitors: a molecular dynamics investigation.

(2014) PLoS One 9

PubMed: 24466056 | PubMedCentral: PMC3895040 | DOI: 10.1371/journal.pone.0086365

[17] The closure of a mobile loop (residues 96–107; residue numbering refers to human LDHA in PDB 1I10), in which the conserved Arg105 could stabilize the transition state in the hydride-trans... er reaction, is indispensible for catalytic activity.

[17] Yet, the first human LDHA structure (PDB 1I10), in complex with a substrate mimic (oxamate) and the cofactor NADH, shows that the mobile loop of one of the four identical monomers, chain D, is in an open conformation, indicating certain probability of the loop being open.

[37] After removing all non-protein residues, chain A (loop closed) and chain D (loop open) of PDB 1I10 was used as the macromolecular model for the docking into the adenine pocket and substrate/nicotinamide pocket, respectively.

g001 Figure 1 Structure of human LDHA (PDB 1I10).

The docking poses with the best overlap with NADH adenine (as in PDB 1I10 chain D) were selected for adenine pocket docking, while those having the best interaction between ligand carboxylate and Arg168 guanidinium group were chosen for substrate/nicotinamide pocket docking.

Representative structures of the monomeric (carbon atoms in magenta) and the tetrameric (carbon atoms in cyan) forms are overlaid with the crystal structure (PDB 1I10, carbon atoms in grey).

The starting structure of the LDHA:PYR-NADH system was built by altering the oxamate in PDB 1I10 to pyruvate.

For apo LDHA, the starting structure was directly extracted from PDB 1I10 (chains A, B, C, and D) after removal of non-protein residues.

The Mobile Loop While the initial structures of LDHA:0SN and LDHA:1E4 systems were built with all mobile loops closed (from PDB 4AJP), all other LDHA:ligand systems had the mobile loop of chain D initially open (from PDB 1I10).

The initial structures of LDHA:1E7, LDHA:AJ1, LDHA:2B4, and LDHA:6P3 complexes were constructed by fitting the ligand structure (from chain A of PDBs 4I9U, 4AJ1, 4AJE, and 4I8X, respectively) analogously into the binding sites of human LDHA from PDB 1I10 (chains A, B, C, and D).

Table S3 Root mean squared deviations (RMSD) between PDB 1I10 and PDB 4AJP.

B) Overlay of representative MD structures from four monomers of LDHA:FX11 A (carbon atoms in cyan, magenta, yellow, and pink, respectively) and PDB 1I10 (carbon atoms in grey).

Materials and Methods System Preparation Two crystal structures of human LDHA [17] , [18] (PDBs 1I10 and 4AJP) have been used in MD simulations, and their structures are very similar ( Table S3 ).

Publication Year: 2014

Structural characterization of the apo form and NADH binary complex of human lactate dehydrogenase.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24816116 | PubMedCentral: PMC4014127 | DOI: 10.1107/S1399004714005422

Figure 4 Superposition of the human LDH-A apo form (grey) and NADH binary complex (purple) reported here with the ternary complex bound to NADH and the competitive inhibitor oxamate (two different mon... mers shown in blue and light blue, respectively; PDB entry 1i10 ; Read et al. , 2001 ▶ ), highlighting the conformational changes upon cofactor and substrate binding, with key residues shown in stick representation.

Comparison between the apo and binary and ternary complex structures   The apo and binary NADH-bound structures presented here in combination with the previously determined ternary complex (PDB entry 1i10 ; Read et al. , 2001 ▶ ) allow a direct comparison between the apo and NADH-bound binary and ternary complex structures of human lactate dehydrogenase A.

In one monomer of the ternary NADH/oxamate structure the active site is substantially more open (PDB entry 1i10 chain D ; Read et al. , 2001 ▶ ), possibly capturing an intermediate conformational state before loop closure.

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4396556

Molecular Docking The X-ray crystal structure of human LDH (M form), predominantly found in human muscle, was downloaded from the RCSB protein data bank (PDB: 1I10).

Thus optimized compound PGG was docked in the catalytic active site of the chain A of the LDH protein complex (PDB: 1I10) using high precision Surlex-Dock GeomX program as implemented in Sybyl software by incremental construction approach of building the structure in the active site so as to favor the binding affinity.

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4463413

The ensemble of closed conformations was generated by superimposing subunits of the structures 1i10 (A–C, E, F, H) and 4ajp (A–D) The conformational variability of the loop 96–... 11 in the open state complicates the choice of an appropriate structure for modeling and virtual screening.

Orange denotes the coordinates of compounds in the crystal structures 1i10 and 4ajp Accounting for loop 96–111 interactions Computer-aided screening with the generated LDH-A models should take into consideration interactions between substrates/inhibitors and the loop 96–111, which stabilized the closed conformation state.

On the basis of the crystal tetrameric structure 1i10, we constructed full-atom models of human LDH-A (in complex with NADH and in the apo form) that showed promise in virtual screening of a low-molecular-weight compound library.

The 1i10 structure at 2.30 A resolution is complexed with NADH and oxamate, and the 4ajp structure at 2.38 A resolution is complexed with the highly potent inhibitor 88N occupying the substrateand coenzyme-binding sites.

To identify hydrogen bonding and hydrophobic interactions that are formed upon loop closure, we compared structures of the apo form 4l4r and those of the enzyme-inhibitor complexes 1i10 and 4ajp.

RMS deviation values of the docking poses of inhibitors were calculated using reference coordinates obtained from the 1i10 and 4ajp structures (subunit A).

The 1i10 structure was chosen for further modeling due to high resolution and the presence of coordinates of all residues within the tetramer.

To analyze the conformational space of the flexible loop 96–111, we superimposed individual subunits of these structures onto the subunit A of the 1i10 structure using Cα-atoms.

Construction of full-atom enzyme models Hydrogen atoms were added to the tetrameric LDH-A molecule derived from 1i10.

The structure of human LDH-A crystallized as a ternary complex in the presence of NADH and oxamate (PDB ID 1i10) shows that transition of the loop 96-111 from the open to the closed form may not necessarily occur following substrate binding [ 7 ].

RESULTS AND DISCUSSION Crystal structure selection The Protein Data Bank contains the following human LDH-A structures: the apo form (PDB ID 4l4r), the binary complex with NADH (4l4s), and complexes with inhibitors in the open (4jnk, 4m49, 4qo7, 4qo8) and closed (1i10, 4ajp) conformational states.

Publication Year: 2015