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Cheminformatics-based drug design approach for identification of inhibitors targeting the characteristic residues of MMP-13 hemopexin domain.
(2010) PLoS One 5
PubMed: 20824169 | PubMedCentral: PMC2930869 | DOI: 10.1371/journal.pone.0012494
The better resolution 3D structure for MMP-1 (1SU3 with catalytic and Hpx domains) and -8 (1BZS, only containing catalytic domain; no structure available with Hpx domain) obtained from PDB were used f... r the docking.
1SU3 structure contains both Hpx and catalytic domains, while 1BZS has only the catalytic domain.
Table S3 The 25 screened ligands that interact with at least one residue of the HCR-13 pf of MMP-13 (PDB ID: 1PEX) and their hydrogen bond interaction(s) to residues of MMP-1 (PDB ID: 1SU3) and -8 (PDB ID: 1BZS).
Publication Year: 2010
Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering.
(2010) BMC Bioinformatics 11
PubMed: 20932281 | PubMedCentral: PMC3098083 | DOI: 10.1186/1471-2105-11-500
sub-families classes PDB codes archetypal MMPs MMP-1 1CGE, 966C, 1HFC, 2TCL, 1CGL, 1CGF, 2J0T Collagenasi MMP-8 1MNC, 1ZS0, 1ZP5, 1MMB, 1JAO, 1JAP, 1JAQ, 1JJ9, 1I76, 1I73, 1ZVX, 1BZS, 1KBC, 1JAN, 1A86... 1A85, 1JH1, 3DNG, 3DPE, 3DPF, 2OY2, 2OY4 MMP-13 1XUC, 1XUR, 1XUD, 1YOU, 830C, 456C, 1ZTQ, 2D1N, 1CXV, 2PJT, 2OW9, 2E2D, 2OZR metallo-elastase MMP-12 1Y93, 1RMZ, 1OS9, 1OS2, 1UTZ, 1UTT, 1JIZ, 1ROS, 1JK3, 3F15, 3F16, 3F17, 3F18, 3F19, 3F1A, 2W0D, 2HU6, 2OXU, 2OXW, 2OXZ Stromelysin MMP-3 1B8Y, 1CIZ, 1CAQ, 1G4K, 2USN, 1USN, 1SLM, 1UEA, 1HFS, 1QIC, 1C3I, 1CQR, 1BQO, 1BIW, 1SLN, 1HY7, 1G05, 1G49, 1D5J, 1D8F, 1D7X, 1D8M, 2D1O, 1B3D, 1QIA, 1C8T MMP-10 1Q3A matrilysin Matrilysin MMP-7 1MMP, 1MMQ, 1MMR gelatinases Gelatinase MMP-9 1GKC, 1GKD, 2OVX, 2OVZ, 2OW0, 2OW1, 2OW2 MMP-2 1QIB convertase-activatable MMPs MT-MMPs MMP-14 1BUV, 1BQQ MMP-16 1RM8 stromelysin-3 MMP-11 1HV5 After removing water molecules and co-crystallised inhibitors, MMPs were aligned onto Cartesian coordinates of C-alpha atoms and the three catalytic histidine side chains of 1ZS0, selected as template.
Insight towards the conserved water mediated recognition of catalytic and structural Zn(+2) ions in human Matrix Metalloproteinase-8 enzyme: A study by MD-simulation methods.
(2013) Bioinformation 9
PubMed: 23423544 | PubMedCentral: PMC3569599 | DOI: 10.6026/97320630009126
Identification of conserved water molecules : To identify the conserved water molecules in hMMP-8, the five different X-ray crystal structures of the protein (1BZS, 1JAP, 1ZP5, 1ZVX, 1ZSO) were compar... d using 1BZS as template.
Again, after energy minimization of the two (1BZS, 1JAP) solvated PDB structures two incoming water molecules are observed at the same hydrophilic WH and WI sites which are included in Table 3 .
Methodology X-ray structures of hMMP–8 (1BZS, 1JAP, 1ZP5, 1ZVX, 1ZSO) were taken from Protein Data Bank [ 11 – 13 ].
In the energy minimized native 1BZS, 1JAP, 1ZVX crystal structures, two incoming water molecules (W H and W I ) form bond with ZnC, and WH also forms H–bond to E 198 (2.5 to 3.5 Å).
The coordination of water molecules present at W H hydrophilic site which forms H-bond to E 198 around ZnC ion in three Emin X-ray structures (1BZS, 1JAP, 1ZVX) and all MD simulated structures are observed to be conserved.
The crystallographic structures (1BZS, 1JAP, 1ZP5, 1ZVX, 1ZSO) [ 4 – 8 ] of hMMP-8 Table 1 (see supplementary material) have explored the presence of two (catalytic and structural) zinc ions in catalytic domains of enzyme.
In all the simulated X- ray and solvated structures of hMMP–8 (1BZS, 1JAP, 1ZP5, 1ZVX, 1ZSO) the ZnS atom is coordinated by two positionally conserved water molecule (W and WS) and three histidine and one aspartic acid residue.
The average binding free energy of ZnC and ZnS ions in the five PDB structures (1BZS, 1JAP, 1ZP5, 1ZVX, 1ZSO) are 23.88 and 137.1 Kcal/mole, whereas after simulation the values are reduced to -75.7 and -34.5 Kcal/mole.
The average electrostatic binding free energy of ZnC and ZnS ions of the five PDB structures (1BZS, 1JAP, 1ZP5, 1ZVX, 1ZSO) are -0.848 and -0.682 Kcal/mole respectively, whereas after simulation the values are -6.0 and -10.2 Kcal/mole.
Publication Year: 2013
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