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Open data
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Basic information
Entry | Database: PDB / ID: 1gmd | ||||||
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Title | X-ray crystal structure of gamma-chymotrypsin in hexane | ||||||
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![]() | HYDROLASE / SERINE PROTEASE | ||||||
Function / homology | ![]() chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Yennawar, N.H. / Yennawar, H.P. / Banerjee, S. / Farber, G.K. | ||||||
![]() | ![]() Title: X-ray crystal structure of gamma-chymotrypsin in hexane. Authors: Yennawar, N.H. / Yennawar, H.P. / Farber, G.K. | ||||||
History |
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Remark 700 | SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA BARRELS. THIS IS REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.5 KB | Display | ![]() |
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PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 406.8 KB | Display | ![]() |
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Full document | ![]() | 414.6 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-GAMMA-CHYMOTRYPSIN ... , 3 types, 3 molecules EFG
#1: Protein/peptide | Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules B
#4: Protein/peptide | Mass: 521.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 2 types, 137 molecules ![](data/chem/img/HEX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HEX / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | RESIDUES 500 - 505 ARE A PENTAPEPTIDE IN THE ACTIVE SITE AS A TETRAHEDRAL INTERMEDIATE. C OF ...RESIDUES 500 - 505 ARE A PENTAPEPTI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.85 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.6 / Method: batch methodDetails: referred to 'Stoddard, B. L.', (1990) Biochemistry, 29, 4871-4879 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. obs: 7606 / Observed criterion σ(I): 2 / Num. measured all: 13982 / Rmerge(I) obs: 0.092 |
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Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.176 / Rfactor obs: 0.176 / Highest resolution: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 5 Å / Rfactor obs: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.82 |