3COG

Crystal structure of human cystathionase (Cystathionine gamma lyase) in complex with DL-propargylglycine

Structural Biology Knowledgebase: 3COG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.158

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3COG

Classification: LYASE

Total Structure Weight: 179183.84

Macromolecule Entities
Molecule Chains Length Organism Details
Cystathionine gamma-lyase A, B, C, D 403 Homo sapiens EC#: 4.4.1.1 IUBMB
Gene Name(s): CTH Gene View

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PLP
Query on PLP

A, C, D PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
2AG
Query on 2AG

A, C, D (2S)-2-aminopent-4-enoic acid
L-allylglycine (Synonym)
C5 H9 N O2
WNNNWFKQCKFSDK-BYPYZUCNSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A, C, D NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.158
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 105.35 α = 90.00
b = 107.22 β = 90.00
c = 153.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-28
  • Released Date: 2008-05-27
  • Deposition author(s): Collins, R., Karlberg, T., Lehtio, L., Arrowsmith, C.H., Berglund, H., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Olesen, K., Persson, C., Schuler, H., Svensson, L., Thorsell, A.G., Tresaugues, L., Van den Berg, S., Sagermark, J., Busam, R.D., Welin, M., Weigelt, J., Wikstrom, M., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4