2FFD | pdb_00002ffd

Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE

PDB DOI: https://doi.org/10.2210/pdb2FFD/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2005-12-19 Released: 2006-07-04
Deposition Author(s): Betts, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.268 (Depositor), 0.266 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

The structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE.

Betts, L., Merenbloom, B.K., Lord, S.T.

(2006) Thromb Haemost 4: 1139-1141

PubMed: 16689770 Search on PubMed
DOI: https://doi.org/10.1111/j.1538-7836.2006.01902.x
Primary Citation Related Structures:
2FFD

Macromolecule Content

Total Structure Weight: 161.74 kDa
Atom Count: 10,894
Modeled Residue Count: 1,319
Deposited Residue Count: 1,404
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen alpha/alpha-E Chain	A, D	66	Homo sapiens	Mutation(s): 0 Gene Names: FGA
UniProt & NIH Common Fund Data Resources
Find proteins for P02671 (Homo sapiens) Explore P02671 Go to UniProtKB: P02671
PHAROS: P02671 GTEx: ENSG00000171560
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02671
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta chain	B, E	313	Homo sapiens	Mutation(s): 0 Gene Names: FGB
UniProt & NIH Common Fund Data Resources
Find proteins for P02675 (Homo sapiens) Explore P02675 Go to UniProtKB: P02675
PHAROS: P02675 GTEx: ENSG00000171564
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02675
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain E	Go to GlyGen: P02675-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen gamma chain	C, F	311	Homo sapiens	Mutation(s): 0 Gene Names: FGG
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens) Explore P02679 Go to UniProtKB: P02679
PHAROS: P02679 GTEx: ENSG00000171557
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02679
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-PRO-ARG-VAL-VAL-GLU peptide	G, H, I, J	6	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K, L	3		N-Glycosylation	Interactions Focus chain K Focus chain L Interactions & Density Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain M [auth B]	M [auth B], N [auth C], O [auth E], P [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth E] Focus chain P [auth F] Interactions & Density Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth E] Focus chain P [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.268 (Depositor), 0.266 (DCC)
R-Value Work: 0.211 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.521	α = 90
b = 94.652	β = 90
c = 227.49	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-07-04

Deposition Author(s):

Betts, L.

Revision History (Full details and data files)

Version 1.0: 2006-07-04
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary