1M1J

Crystal structure of native chicken fibrinogen with two different bound ligands

PDB DOI: https://doi.org/10.2210/pdb1M1J/pdb
Entry: 1M1J supersedes: 1JFE

Classification: BLOOD CLOTTING
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2002-06-19 Released: 2002-06-26
Deposition Author(s): Yang, Z., Kollman, J.M., Pandi, L., Doolittle, R.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256
R-Value Work: 0.227

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 311.78 kDa
Atom Count: 16,117
Modelled Residue Count: 1,984
Deposited Residue Count: 2,744
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen alpha subunit	A, D	491	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for P14448 (Gallus gallus) Explore P14448 Go to UniProtKB: P14448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14448
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta chain	B, E	464	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for Q02020 (Gallus gallus) Explore Q02020 Go to UniProtKB: Q02020
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02020
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen gamma chain	C, F	409	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for O93568 (Gallus gallus) Explore O93568 Go to UniProtKB: O93568
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O93568
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-PRO-ARG-PRO peptide	G, H	4	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-HIS-ARG-PRO peptide	I, J	4	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain S [auth F] SDF format, chain U [auth I] MOL2 format, chain N [auth C] MOL2 format, chain S [auth F] MOL2 format, chain U [auth I]	N [auth C], S [auth F], U [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth C] Focus chain S [auth F] Focus chain U [auth I]
NDG Query on NDG Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain V [auth J] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain V [auth J]	K [auth B], M [auth C], P [auth E], R [auth F], V [auth J]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth E] Focus chain R [auth F] Focus chain V [auth J]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain Q [auth E] SDF format, chain L [auth B] SDF format, chain T [auth F] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain L [auth B] MOL2 format, chain T [auth F]	L [auth B], O [auth C], Q [auth E], T [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth E] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256
R-Value Work: 0.227
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.09	α = 90
b = 100.02	β = 105.79
c = 200.09	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-06-26

Deposition Author(s):

This entry supersedes: 1JFE

Revision History (Full details and data files)

Version 1.0: 2002-06-26
Type: Initial release
Version 1.1: 2008-04-28
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: Atomic model, Data collection, Derived calculations, Structure summary