6M8P

Human ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.286 

wwPDB Validation   3D Report Full Report



Literature

Conformational transitions drive ERAP1 catalytic cycle and explain the effect of disease-correlated polymorphism.

Maben, Z., Stern, L.J.

To be published.

Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoplasmic reticulum aminopeptidase 1A, B, C, D, E, F, G, H, A,  B,  C,  D,  E,  F,  G,  H,  I,  J,  K,  L,  M,  N,  O,  P,  Q,  R,  S,  T,  U,  V
899Homo sapiensMutation(s): 0 
Gene Names: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154
EC: 3.4.11
Find proteins for Q9NZ08 (Homo sapiens)
Explore Q9NZ08 
Go to UniProtKB:  Q9NZ08
NIH Common Fund Data Resources
PHAROS:  Q9NZ08
GTEx:  ENSG00000164307
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, AA, BA, CA, DA, W, X, Y, Z, 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
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P52
Query on P52
Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide
C27 H37 N4 O4 P
QKFOTLXPIIESQI-IEZKXTBUSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P52IC50:  48   nM  BindingDB
P52IC50:  33   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.286 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.79α = 90
b = 548.684β = 90
c = 589.056γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-22 
  • Released Date: 2019-12-18 
    • Deposition Author(s): Maben, Z., Stern, L.J.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01AI038996

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary