2ffd

Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fibrinogen alpha/alpha-E Chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Fibrinogen beta chain × 1 （P02675） Fibrinogen gamma chain × 1 （P02679） GLY-PRO-ARG-VAL-VAL-GLU peptide × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 5 其他Polymer 1	Fibrinogen beta chain × 1 （P02675） Fibrinogen gamma chain × 1 （P02679） GLY-PRO-ARG-VAL-VAL-GLU peptide × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FIBA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–66； UniProt 145–210 Author chain D； PDBConstruct 1–66； UniProt 145–210

Fibrinogen beta chain

Homo sapiens

UniProt P02675

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Fibrinogen alpha/alpha-E Chain × 1 （P02671） Fibrinogen gamma chain × 1 （P02679） GLY-PRO-ARG-VAL-VAL-GLU peptide × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 5 其他Polymer 1	Fibrinogen alpha/alpha-E Chain × 1 （P02671） Fibrinogen gamma chain × 1 （P02679） GLY-PRO-ARG-VAL-VAL-GLU peptide × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FIBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–313； UniProt 187–499 Author chain E； PDBConstruct 1–313； UniProt 187–499

Fibrinogen gamma chain

Homo sapiens

UniProt P02679

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Fibrinogen alpha/alpha-E Chain × 1 （P02671） Fibrinogen beta chain × 1 （P02675） GLY-PRO-ARG-VAL-VAL-GLU peptide × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 5 其他Polymer 1	Fibrinogen alpha/alpha-E Chain × 1 （P02671） Fibrinogen beta chain × 1 （P02675） GLY-PRO-ARG-VAL-VAL-GLU peptide × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FIBG_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–311； UniProt 122–432 Author chain F； PDBConstruct 1–311； UniProt 122–432

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ffd
Deposition date deposition_date	2005-12-19
Structure title title	Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE
Keywords keywords	;Complex of fibrinogen with "A" site mimic GPRVVE in both "A" and "B" sites, BLOOD CLOTTING ;; BLOOD CLOTTING
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2ffd__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ffd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ffd__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.71 Å
Rg (electron density)	33.17 Å
Total Rg	33.41 Å
Atom count	5447
Residues	674
Excluded volume	95797 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ffd__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ffd__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Fibrinogen alpha/alpha-E Chain
Molecular weight formula_weight	7747.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	10894

VIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALAREVDLKDYEDQQKQLEQVIAK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Fibrinogen beta chain
Molecular weight formula_weight	35940.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

HQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYCRTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQNRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIEMEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGMFFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDDGVVWMNWKGSWYSMRKMSMKIRPFFPQQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Fibrinogen gamma chain
Molecular weight formula_weight	35218.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

YEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNWIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVGPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAEQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIPFNRLTIGEGQQHHLGGAK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 4 Entity 4 polymer

Description description	GLY-PRO-ARG-VAL-VAL-GLU peptide
Molecular weight formula_weight	656.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J

GPRVVE

Entity 5 Entity 5 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ffda1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
Family Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

Domain ID domain_id	d2ffdd1
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
Family Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

CATH v4.4 (14 domains)

Domain ID domain_id	2ffdA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2ffdB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2ffdB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	2ffdB03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

Domain ID domain_id	2ffdC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2ffdC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	2ffdC03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

Domain ID domain_id	2ffdD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2ffdE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2ffdE02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	2ffdE03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

Domain ID domain_id	2ffdF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2ffdF02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

Domain ID domain_id	2ffdF03
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

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Unit-cell length a length_a	89.521 Å
Unit-cell length b length_b	94.652 Å
Unit-cell length c length_c	227.490 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2140
R_work r_work	0.2110
R_free r_free	0.2680

Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Fibrinogen alpha/alpha-E Chain

State in the Current Structure

Other States of the Same Protein in the Database

Fibrinogen beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Fibrinogen gamma chain

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ffd__assembly_1__model_1

2ffd__assembly_1__model_1 | I(q)

2ffd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (2 domains)

CATH v4.4 (14 domains)

7. Citations (1)

Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE

1. Protein Identity and Related Structures Protein Identity & Related Structures

Fibrinogen alpha/alpha-E Chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fibrinogen beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Fibrinogen gamma chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ffd__assembly_1__model_1

2ffd__assembly_1__model_1 | I(q)

2ffd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (2 domains)

CATH v4.4 (14 domains)

7. Citations (1)