5W0U

Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.251

Literature

Macromolecules
Sequence Display for 5W0U

Classification: HYDROLASE / DNA

Total Structure Weight: 131563.03


Macromolecule Entities
Molecule Chains Length Organism Details
Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase A, B 549 Escherichia coli Homo sapiens EC#: 3.5.4.38 IUBMB
Fragment: UNP residues 27-392,UNP residues 13-181
Mutation: D83A, K84A, E173A, N174A, K240A, E360A, K363A, D364A, F1042E, E1058A, H1130A, R1131E, F1141Y, F1145E, L1181Q
Gene Name(s): malE Z5632 ECs5017 AICDA Gene View AID
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3') D 12 Homo sapiens
DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3') G 12 Homo sapiens

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

A, B 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.251
  • Space Group: P 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 125.00 α = 90.00
b = 39.78 β = 90.14
c = 153.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-05-31
  • Released Date: 2017-08-16
  • Deposition author(s): Qiao, Q., Wang, L., Wu, H.

Revision History

  • Version 1_0: 2017-08-16

    Type: Initial release