2hod

Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide

Method: X-RAY DIFFRACTION

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

Fibrinogen alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen beta chain × 1 （P02675） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen beta chain × 1 （P02675） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen beta chain × 1 （P02675） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen beta chain × 1 （P02675） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3	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 1–87； UniProt 130–216 Author chain D； PDBConstruct 1–87； UniProt 130–216 Author chain G； PDBConstruct 1–87； UniProt 130–216 Author chain J； 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	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen alpha chain × 1 （P02671） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen alpha chain × 1 （P02671） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen alpha chain × 1 （P02671） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen alpha chain × 1 （P02671） Fibrinogen, gamma polypeptide × 1 （Q53Y18） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3	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 1–328； UniProt 164–491 Author chain E； PDBConstruct 1–328； UniProt 164–491 Author chain H； PDBConstruct 1–328； UniProt 164–491 Author chain K； PDBConstruct 1–328； UniProt 164–491

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	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen alpha chain × 1 （P02671） Fibrinogen beta chain × 1 （P02675） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen alpha chain × 1 （P02671） Fibrinogen beta chain × 1 （P02675） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen alpha chain × 1 （P02671） Fibrinogen beta chain × 1 （P02675） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 5	Fibrinogen alpha chain × 1 （P02671） Fibrinogen beta chain × 1 （P02675） Gly-hydroxyPro-Arg-Pro-amide peptide ligand × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q53Y18_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–323； UniProt 115–437 Author chain F； PDBConstruct 1–323； UniProt 115–437 Author chain I； PDBConstruct 1–323； UniProt 115–437 Author chain L； PDBConstruct 1–323； UniProt 115–437

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_id	2hod
Deposition date deposition_date	2006-07-14
Structure title title	Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide
Keywords keywords	Knob-hole interactions, BLOOD CLOTTING-PEPTIDE complex; BLOOD CLOTTING/PEPTIDE
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.

2hod__assembly_1__model_1

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

Download this curve (.dat)

2hod__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hod__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.14 Å
Rg (electron density)	34.94 Å
Total Rg	35.13 Å
Atom count	5594
Residues	692
Excluded volume	98456 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hod__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2hod__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2hod__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2hod__assembly_4__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 (6)

Entity 1 Entity 1 polymer

Description description	Fibrinogen alpha chain
Molecular weight formula_weight	10245.0 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	22278

VSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALAREVDLKDYEDQQKQLEQVIAKDLLPSR

Entity 2 Entity 2 polymer

Description description	Fibrinogen beta chain
Molecular weight formula_weight	37692.0 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

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

DNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYCRTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQNRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIEMEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGMFFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDDGVVWMNWKGSWYSMRKMSMKIRPFFPQQ

Entity 3 Entity 3 polymer

Description description	Fibrinogen, gamma polypeptide
Molecular weight formula_weight	36564.6 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

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

MLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNWIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVGPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAEQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIPFNRLTIGEGQQHHLGGAKQAGDV

Entity 4 Entity 4 polymer

Description description	Gly-hydroxyPro-Arg-Pro-amide peptide ligand
Molecular weight formula_weight	440.5 kDa
Source method src_method	syn
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P,Q,R,S,T

GPRPX

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

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	10

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2hoda1
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	d2hodd1
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	d2hodg1
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	d2hodj1
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 (24 domains)

Domain ID domain_id	2hodA00
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	2hodB01
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	2hodB02
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	2hodB03
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	2hodC01
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	2hodC02
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	2hodD00
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	2hodE01
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	2hodE02
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	2hodE03
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	2hodF01
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	2hodF02
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	2hodG00
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	2hodH01
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	2hodH02
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	2hodH03
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	2hodI01
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	2hodI02
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	2hodJ00
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	2hodK01
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	2hodK02
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	2hodK03
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	2hodL01
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	2hodL02
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	81.647 Å
Unit-cell length b length_b	47.069 Å
Unit-cell length c length_c	431.460 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2384
R_work r_work	0.2676
R_free r_free	0.3471

Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide

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

Fibrinogen alpha 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 polypeptide

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

2hod__assembly_1__model_1

2hod__assembly_1__model_1 | I(q)

2hod__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (4 domains)

CATH v4.4 (24 domains)

7. Citations (0)

Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide

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

Fibrinogen alpha 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 polypeptide

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

2hod__assembly_1__model_1

2hod__assembly_1__model_1 | I(q)

2hod__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (4 domains)

CATH v4.4 (24 domains)

7. Citations (0)