4APZ

Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1

Structural Biology Knowledgebase: 4APZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4APZ

Classification: HYDROLASE

Total Structure Weight: 809486.88

Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF 1, 2, 3..., 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m 144 Bacillus subtilis EC#: 3.6.1.23 IUBMB
Gene Name(s): yncF BSU17660
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m 2'-DEOXYURIDINE
C9 H12 N2 O5
MXHRCPNRJAMMIM-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
POP
Query on POP

1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

e, l PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.169
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.06 α = 89.72
b = 97.07 β = 88.47
c = 193.85 γ = 90.11

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-11
  • Released Date: 2013-04-24
  • Deposition author(s): Garcia-Nafria, J., Timm, J., Harrison, C., Turkenburg, J.P., Wilson, K.S.

Revision History

  • 2013-08-07
    Type: Citation | Details: JRNL
  • 2013-07-31
    Type: Entry authorship | Details: AUTHOR
  • 2013-07-31
    Type: Atom nomenclature | Details: HETATM
  • 2013-07-31
    Type: Linkage | Details: CONECT
  • 2013-07-31
    Type: Other | Details: MASTER
  • 2013-07-31
    Type: Citation | Details: JRNL
  • 2013-05-22
    Type: Atom nomenclature | Details: HETATM
  • 2013-05-22
    Type: Non-polymer description | Details: REMARK 620
  • 2013-05-22
    Type: Other | Details: MASTER
  • 2013-05-22
    Type: Geometry validation | Details: REMARK 500
  • 2013-05-22
    Type: Linkage | Details: CONECT, LINK
  • 2013-05-22
    Type: Binding sites and description | Details: SITE