2XYD

human Angiotenisn converting enzyme N-domain in complex with Phosphinic tripeptide

Structural Biology Knowledgebase: 2XYD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XYD

Classification: HYDROLASE

Total Structure Weight: 146470.89

Macromolecule Entities
Molecule Chains Length Organism Details
ANGIOTENSIN-CONVERTING ENZYME A, B 610 Homo sapiens EC#: 3.2.1 IUBMB 3.4.15.1 IUBMB
Fragment: RESIDUES 30-639
Mutation: N9Q, N25Q, N82Q, N117Q, N289Q, Q545R, P576L
Details: FINAL CONSTRUCT IS UNDERGLYCOSYALTED MUTANT AND CONTAINS TWO MISMATCH MUTATIONS, P576L AND Q545R
Gene Name(s): ACE Gene View DCP DCP1

Small Molecules
Ligands 9 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
3ES
Query on 3ES

A, B [(2S)-2-({3-[HYDROXYL(2-PHENYL-(1R)-1-{[(BENZYLOXY)[(2S)- 2-({3-[HYDROXYL(2-PHENYL-(1R)-1-CARBONYL]- AMINO}ETHYL)PHOSPHINYL]-2-[(3-PHENYLISOXAZOL- 5-YL)METHYL]-1-OXO-PROPYL}AMINO)-3-(4-HYDROXY- PHENYL)
C38 H38 N3 O9 P
ZPFSKFCSVXPMBD-PFESQZPFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
P6G
Query on P6G

B HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400 (Synonym)
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

A, B TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

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

A, B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

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

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

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3ES N/A in BindingDB
Ki: 180 nM  BindingMOAD
Ki: 150 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.220
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 72.84 α = 89.11
b = 76.44 β = 64.43
c = 82.95 γ = 75.87

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-11-17
  • Released Date: 2011-05-11
  • Deposition author(s): Akif, M., Schwager, S.L., Anthony, C.S., Czarny, B., Beau, F., Dive, V., Sturrock, E.D., Acharya, K.R.

Revision History

  • 2012-04-11
    Type: Non-polymer description | Details: REMARK 630
  • 2012-04-11
    Type: Version format compliance | Details: REMARK 4