1LWU

Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen alpha-1 chain
A, D, G, J
119Petromyzon marinusMutation(s): 0 
UniProt
Find proteins for P02674 (Petromyzon marinus)
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UniProt GroupP02674
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen beta chain
B, E, H, K
323Petromyzon marinusMutation(s): 0 
UniProt
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UniProt GroupP02678
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen gamma chain
C, F, I, L
323Petromyzon marinusMutation(s): 0 
UniProt
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UniProt GroupP04115
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide Ligand Gly-His-Arg-Pro-NH2
M, N, O, P
5N/AMutation(s): 0 
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Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Q
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

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AB [auth O]
HA [auth H]
IA [auth H]
MA [auth H]
R [auth B]
AB [auth O],
HA [auth H],
IA [auth H],
MA [auth H],
R [auth B],
TA [auth K],
XA [auth M],
Y [auth D],
YA [auth N]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG
Query on NAG

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DA [auth F]
EA [auth F]
PA [auth I]
QA [auth I]
U [auth C]
DA [auth F],
EA [auth F],
PA [auth I],
QA [auth I],
U [auth C],
V [auth C],
Z [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GAL
Query on GAL

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NA [auth H]beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
BMA
Query on BMA

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AA [auth E],
KA [auth H]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN
Query on MAN

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BA [auth E]
BB [auth P]
FA [auth F]
JA [auth H]
LA [auth H]
BA [auth E],
BB [auth P],
FA [auth F],
JA [auth H],
LA [auth H],
S [auth B],
SA [auth J],
VA [auth L],
W [auth C],
ZA [auth N]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA
Query on CA

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CA [auth E]
GA [auth F]
OA [auth H]
RA [auth I]
T [auth B]
CA [auth E],
GA [auth F],
OA [auth H],
RA [auth I],
T [auth B],
UA [auth K],
WA [auth L],
X [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.251 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.735α = 88.81
b = 47.654β = 97.23
c = 244.65γ = 86.17
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-23
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2021-10-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary