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Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.
(2008) BMC Struct Biol 8
PubMed: 18954462 | PubMedCentral: PMC2626596 | DOI: 10.1186/1472-6807-8-45
The ROC curves for retrieval of heme binding surfaces querying myoglobin from P. catodon (PDB: 1mbn ) against the GPSS library (h).
A visual depiction of an alignment between the heme binding pockets of myoglobin from P. catodon (PDB: 1mbn ) and structural genomics target hemoglobin alpha-1 (PDB: 1xq5 ) is shown in Figure 3 .
Using myoglobin from P. catodon (PDB: 1mbn , Figure 7ab ) as a query protein, we compared it to a non-redundant (<95% sequence identity) PDB set using BLAST[ 47 ].
Surfaces from myoglobin (CATH code = 1.10.490.10, PDB: 1mbn ), nitrophorin (CATH code = 188.8.131.52, PDB: 1np4 ), and inducible nitric oxide synthase (iNOS) (CATH code = 3.90.1230.10, PDB: 4nos )[ 46 ], representing extrema of heme binding, are shown in Figure 7 .
Heme binding proteins myoglobin (a, CATH code = 1.10.490.10, PDB: 1mbn ), nitrophorin (c, CATH code = 184.108.40.206, PDB: 1np4 ), and inducible nitric oxide synthase (iNOS) (e, CATH code = 3.90.1230.10, PDB: 4nos )[ 46 ].
Publication Year: 2008
Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C.
(2011) J Synchrotron Radiat 18
PubMed: 21525643 | PubMedCentral: PMC3083912 | DOI: 10.1107/S0909049511006315
It was released in 1976 with the file name 1mbn , 14 years after he received the Nobel Prize in Chemistry with Max Perutz ‘for their studies of the structures of globular proteins’.
Publication Year: 2011
On the characterization and software implementation of general protein lattice models.
(2013) PLoS One 8
PubMed: 23555684 | PubMedCentral: PMC3612044 | DOI: 10.1371/journal.pone.0059504
In the first chart of Figure 1 , four sample molecules from different classes (all- , all- , , ), identified in PDB as 1MBN, 1GOF, 1BQB, 2FSU are considered.
Publication Year: 2013
Mechanics of proteins with a focus on atomic force microscopy.
(2013) J Nanobiotechnology 11 Suppl 1
PubMed: 24565326 | PubMedCentral: PMC4029730 | DOI: 10.1186/1477-3155-11-S1-S3
C) Cartoon representation of the protein myoglobin (PDB file 1MBN), mainly made of α-helices, showing the heme group as gray spheres and the oxygen molecule in red.
Similar structures to the E-to-H helix unit in the globin-like fold are found in other helical folds.
(2014) Biomolecules 4
PubMed: 24970216 | PubMedCentral: PMC4030988 | DOI: 10.3390/biom4010268
Figure 2 3D structures of ( a ) soybean leghemoglobin (PDB: 1FSL) and ( b ) sperm whale myoglobin (PDB: 1MBN).
The codes of the Protein Data Bank (PDB) are 1FSL and 1MBN, respectively.
The ADMs for soybean leghemoglobin (PDB: 1FSL) and sperm whale myoglobin (PDB: 1MBN) are presented in Figure 4 .
Figure 1 Amino acid sequence alignment of soybean leghemoglobin (PDB: 1FSL) and sperm whale myoglobin (PDB: 1MBN).
Protein(Source, PDB ID) Family Fold Region Hit by DALI Search with the Following Query(Z Score, rmsd (a) ) Leghemoglobin E-to-H (Soy Bean, 1fsl) Myoglobin E- to-H (Sperm Whale, 1mbn) circadian clock protein Kai A ( Synechococcus , 1R8J) Circadian clock protein KaiA, C-terminal domain KaiA/RbsU domain E-to-H helices (4.4, 3.8) E-to-H helices (7.0, 3.3) secretion control protein A chain( Yersinia , 1XL3) LcrE-like Type III secretion system domain EGH helices (2.0, 4.5) FGH helices (4.1, 3.9) cell invasion protein SipA ( Salmonella , 2FM9) SipA N-terminal domain-like SipA N-terminal domain-like E-to-H helices (2.9, 9.3) H helix (3.0, 8.0) transcriptional regulator RHA1_ro04179 ( Rodococcus , 2NP5) Tetracyclin repressor-like, C-terminal domain Tetracyclin repressor-like, C-terminal domain GH helices (4.4, 9.7) GH helices (2.1, 4.7) hypothetical protein AF0060 ( E. coli , 2P06) AF0060-like all-alpha NTP pyrophosphatases GH helices with a part of the E helix (3.2, 4.8) GH helices (3.5, 3.5) (a): rms distance (Å) between the 3D structures of the aligned regions of the query structure and a hit protein.
Protein(Source, PDB) Number of Homologs Number of Conserved Residue Number of Residues Containing E-to-H Helices Leghemoglobin (soybean 1FSl) 45 34 88 Myoglobin (sperm whale 1MBN) 82 38 96 Circadian clock protein KaiA (Synechococcus, 1R8J) 49 50 98 Secretion control protein) A chain (Yersinia, 1XL3) 29 25 76 Cell invasion protein SipA (Salmonella, 2FM9) 6 0 79 Transcriptional regulator RHA1_ro04179 (Rodococcus, 2NP5) 3 0 74 Hypothetical protein AF0060 ( E. coli , 2P06) 0 0 81 Figure 8 Conserved hydrophobic residues in the E-to-H helix unit of ( a ) 1FSL, ( b ) 1MBN, ( c ) 1R8J, ( d ) 1XL3, ( e ) 2FM9, ( f ) 2NP5, and ( g ) 2P06.
Common Residue Patterns Specific to the E-to-H Helix Unit Defined from the Packing Patterns of Conserved Hydrophobic Residues A common residue pattern might be defined from the information of both conserved hydrophobic residues and the packing residues of the E-to-H helix unit in 1FSL, 1MBN, 1R8J and 1XL3.
Publication Year: 2014
The Protein Data Bank archive as an open data resource.
(2014) J Comput Aided Mol Des 28
PubMed: 25062767 | PubMedCentral: PMC4196035 | DOI: 10.1007/s10822-014-9770-y
Early structures included myoglobin ( 1 PDB ID 1mbn [ 6 , 7 ]), the first structure solved by X-ray crystallography, and small enzymes ( 2 top 4pti [ 48 ], bottom right 2cha [ 49 ], bottom left 3cpa [... 50 ]).
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