1B5F

NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.

Structural Biology Knowledgebase: 1B5F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Observed: 0.205

Literature

Macromolecules
Sequence Display for 1B5F

Classification: HYDROLASE

Total Structure Weight: 74386.98

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (CARDOSIN A) A, C 239 Cynara cardunculus EC#: 3.4.23 IUBMB
Details: RESIDUE NAMES ACCORDING TO PEPSIN NUMBERING AFTER A.R.SIELECKI, A.A.FEDOROV, A.BOODHOO, N.S.ANDREEVA, AND M.N.G.JAMES (1990).J.MOL.BIOL. 214, 143-170. NATIVE CARDOSIN A SEQUENCE DIFFERS FROM THAT DEDUCED FROM CDNA THROUGH EXCISION OF THE PSI DOMAIN. MATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. A FIRST, 35 KD CHAIN COMPRISES RESIDUES 0/1 - 238 AND THE SECOND 15 KD CHAIN COMPRISES RESIDUES 243 - 326. THE ASYMMETRIC UNIT CONTAINS TWO CARDOSIN A MOLECULES. MOLECULE 1 HAS BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*, AND MOLECULE 2 HAVE BEEN ASSIGNED CHAIN INDICATORS *C* AND *D*. MOLECULE 1 COMPOSED BY CHAINS A(0-238) AND B (243-326). MOLECULE 2 COMPOSED BY CHAINS C(1-238) AND D (243-326). N-LINKED CARBOHYDRATES (RESIDUES 401-405 A AND 401-406 C) ATTACHED TO ASN 67. N-LINKED CARBOHYDRATES (RESIDUES 501-504 B AND 501-504 D) ATTACHED TO ASN 257.
Gene Name(s): cardA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (CARDOSIN A) B, D 87 Cynara cardunculus EC#: 3.4.23 IUBMB
Details: RESIDUE NAMES ACCORDING TO PEPSIN NUMBERING AFTER A.R.SIELECKI, A.A.FEDOROV, A.BOODHOO, N.S.ANDREEVA, AND M.N.G.JAMES (1990).J.MOL.BIOL. 214, 143-170. NATIVE CARDOSIN A SEQUENCE DIFFERS FROM THAT DEDUCED FROM CDNA THROUGH EXCISION OF THE PSI DOMAIN. MATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A POST-TRANSLATIONAL CLEAVAGE EVENT. A FIRST, 35 KD CHAIN COMPRISES RESIDUES 0/1 - 238 AND THE SECOND 15 KD CHAIN COMPRISES RESIDUES 243 - 326. THE ASYMMETRIC UNIT CONTAINS TWO CARDOSIN A MOLECULES. MOLECULE 1 HAS BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*, AND MOLECULE 2 HAVE BEEN ASSIGNED CHAIN INDICATORS *C* AND *D*. MOLECULE 1 COMPOSED BY CHAINS A(0-238) AND B (243-326). MOLECULE 2 COMPOSED BY CHAINS C(1-238) AND D (243-326). N-LINKED CARBOHYDRATES (RESIDUES 401-405 A AND 401-406 C) ATTACHED TO ASN 67. N-LINKED CARBOHYDRATES (RESIDUES 501-504 B AND 501-504 D) ATTACHED TO ASN 257.
Gene Name(s): cardA

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, B, C BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, C, D ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A, B, C, D ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Observed: 0.205
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 116.96 α = 90.00
b = 87.19 β = 104.43
c = 81.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-01-06
  • Released Date: 1999-01-13
  • Deposition author(s): Frazao, C., Bento, I., Carrondo, M.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values