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2z4e

Crystal Structure of D-Dimer from Human Fibrin Complexed with Gly-His-Arg-Pro-Tyr-amide

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fibrinogen alpha chain

OrganismNot specified

UniProt P02671

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 10 其他Polymer 1 Fibrinogen beta chain × 2 （P02675） Fibrinogen, gamma polypeptide × 2 （Q53Y18） Fibrin B knob (tetrapeptide) × 2 Fibrin B knob (pentapeptide) × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 Consistent with protein count
2 Other combination Heteromer Protein 5 其他Polymer 1 Fibrinogen beta chain × 1 （P02675） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Fibrin B knob (tetrapeptide) × 1 Fibrin B knob (pentapeptide) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 Fibrinogen beta chain × 1 （P02675） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Fibrin B knob (tetrapeptide) × 1 Fibrin B knob (pentapeptide) × 1 CALCIUM ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1bbr 1bbr 1bbr 1bbr 1fza 1fzb 1fzc 1fzd 1fzd 1fze 1fze 1fze

70 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name FIBA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–87； UniProt 130–216 Author chain D； PDBConstruct 1–87； UniProt 130–216

Fibrinogen beta chain

OrganismNot specified

UniProt P02675

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 10 其他Polymer 1 Fibrinogen alpha chain × 2 （P02671） Fibrinogen, gamma polypeptide × 2 （Q53Y18） Fibrin B knob (tetrapeptide) × 2 Fibrin B knob (pentapeptide) × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 Consistent with protein count
2 Other combination Heteromer Protein 5 其他Polymer 1 Fibrinogen alpha chain × 1 （P02671） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Fibrin B knob (tetrapeptide) × 1 Fibrin B knob (pentapeptide) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 Fibrinogen alpha chain × 1 （P02671） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Fibrin B knob (tetrapeptide) × 1 Fibrin B knob (pentapeptide) × 1 CALCIUM ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1fza 1fzb 1fzc 1fze 1fze 1fze 1fzf 1fzg 1lt9 1lt9 1ltj 1ltj

58 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name FIBB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–326； UniProt 164–489 Author chain E； PDBConstruct 1–326； UniProt 164–489

Fibrinogen, gamma polypeptide

OrganismNot specified

UniProt Q53Y18

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 10 其他Polymer 1 Fibrinogen alpha chain × 2 （P02671） Fibrinogen beta chain × 2 （P02675） Fibrin B knob (tetrapeptide) × 2 Fibrin B knob (pentapeptide) × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 Consistent with protein count
2 Other combination Heteromer Protein 5 其他Polymer 1 Fibrinogen alpha chain × 1 （P02671） Fibrinogen beta chain × 1 （P02675） Fibrin B knob (tetrapeptide) × 1 Fibrin B knob (pentapeptide) × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 Fibrinogen alpha chain × 1 （P02671） Fibrinogen beta chain × 1 （P02675） Fibrin B knob (tetrapeptide) × 1 Fibrin B knob (pentapeptide) × 1 CALCIUM ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2hod 2hod 2hod 2hod 2hpc 2hpc 2hpc 2hpc 2q9i 2q9i 2vdo 2vdp

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q53Y18_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–324； UniProt 114–437 Author chain F； PDBConstruct 1–324； UniProt 114–437

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_id2z4e
Deposition date deposition_date2007-06-16
Structure title titleCrystal Structure of D-Dimer from Human Fibrin Complexed with Gly-His-Arg-Pro-Tyr-amide
Keywords keywordsfibrin clots, B-knobs, beta-holes, BLOOD CLOTTING; BLOOD CLOTTING
Experimental Method methodX-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.

2z4e__assembly_1__model_1

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

Download this curve (.dat)

2z4e__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2z4e__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）54.06 Å
Rg (electron density)55.59 Å
Total Rg55.52 Å
Atom count10646
Residues1315
Excluded volume187070 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2z4e__assembly_1__model_1 decameric （10） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2z4e__assembly_2__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2z4e__assembly_3__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 (8)

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id2z4eA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2z4eB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
Domain ID domain_id2z4eB02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
Domain ID domain_id2z4eC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
Domain ID domain_id2z4eC02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
Domain ID domain_id2z4eD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily50 —
Domain ID domain_id2z4eE01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
Domain ID domain_id2z4eE02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
Domain ID domain_id2z4eF01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology215 — Gamma Fibrinogen; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Gamma Fibrinogen, chain A, domain 1
Domain ID domain_id2z4eF02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
Homologous superfamily homologous superfamily10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
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7. Citations (1)