2BGN

HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE IV
A, B, C, D
728Homo sapiensMutation(s): 0 
EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens)
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Go to UniProtKB:  P27487
PHAROS:  P27487
GTEx:  ENSG00000197635 
Entity Groups  
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UniProt GroupP27487
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ADENOSINE DEAMINASE
E, F, G, H
363Bos taurusMutation(s): 3 
EC: 3.5.4.4
UniProt
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UniProt GroupP56658
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TAT PROTEINI [auth W],
J [auth X],
K [auth Y],
L [auth Z]		9Human immunodeficiency virus 1Mutation(s): 1 
UniProt
Find proteins for P12506 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
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Entity Groups  
UniProt GroupP12506
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseM [auth I],
V [auth R]		3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G28454KX
GlyCosmos:  G28454KX
GlyGen:  G28454KX
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
DA [auth d],
N [auth J],
O [auth K],
Q [auth M],
BA [auth b],
DA [auth d],
N [auth J],
O [auth K],
Q [auth M],
S [auth O],
U [auth Q],
W [auth S],
X [auth T],
Z [auth V]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseCA [auth c],
P [auth L],
T [auth P],
Y [auth U]		4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a],
R [auth N]		2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G61843VN
GlyCosmos:  G61843VN
GlyGen:  G61843VN
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
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EA [auth A]
FA [auth A]
GA [auth A]
HA [auth B]
IA [auth B]
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth D],
PA [auth D],
QA [auth D],
RA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
SA [auth E],
TA [auth F],
UA [auth G],
VA [auth H]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.945α = 90
b = 170.273β = 100.93
c = 239.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary