2gc7

Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans.

Method: X-RAY DIFFRACTION

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

Methylamine dehydrogenase light 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 4	Methylamine dehydrogenase heavy chain × 1 Amicyanin × 1 （P22364） Cytochrome c-L × 1 （P29899） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Amicyanin × 1 （P22364） Cytochrome c-L × 1 （P29899） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Amicyanin × 1 （P22364） Cytochrome c-L × 1 （P29899） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Amicyanin × 1 （P22364） Cytochrome c-L × 1 （P29899） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHML_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–131； UniProt 58–188 Author chain F； PDBConstruct 1–131； UniProt 58–188 Author chain J； PDBConstruct 1–131； UniProt 58–188 Author chain N； PDBConstruct 1–131； UniProt 58–188

Amicyanin

OrganismNot specified

UniProt P22364

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Methylamine dehydrogenase light chain × 1 （P22619） Cytochrome c-L × 1 （P29899） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Methylamine dehydrogenase light chain × 1 （P22619） Cytochrome c-L × 1 （P29899） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Methylamine dehydrogenase light chain × 1 （P22619） Cytochrome c-L × 1 （P29899） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Methylamine dehydrogenase light chain × 1 （P22619） Cytochrome c-L × 1 （P29899） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMCY_PARDE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–105； UniProt 27–131 Author chain G； PDBConstruct 1–105； UniProt 27–131 Author chain K； PDBConstruct 1–105； UniProt 27–131 Author chain O； PDBConstruct 1–105； UniProt 27–131

Cytochrome c-L

OrganismNot specified

UniProt P29899

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Methylamine dehydrogenase light chain × 1 （P22619） Amicyanin × 1 （P22364） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Methylamine dehydrogenase light chain × 1 （P22619） Amicyanin × 1 （P22364） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Methylamine dehydrogenase light chain × 1 （P22619） Amicyanin × 1 （P22364） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Methylamine dehydrogenase heavy chain × 1 Methylamine dehydrogenase light chain × 1 （P22619） Amicyanin × 1 （P22364） SODIUM ION × 1 HEME C × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYCL_PARDE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–147； UniProt 23–169 Author chain H； PDBConstruct 1–147； UniProt 23–169 Author chain L； PDBConstruct 1–147； UniProt 23–169 Author chain P； PDBConstruct 1–147； UniProt 23–169

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	2gc7
Deposition date deposition_date	2006-03-13
Structure title title	Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans.
Keywords keywords	Electron transfer, Methylamine dehydrogenase, Cytochrome, amicyanin, Oxidoreductase, Electron transport; Oxidoreductase, Electron transport
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.

2gc7__assembly_1__model_1

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

Download this curve (.dat)

2gc7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gc7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.21 Å
Rg (electron density)	29.53 Å
Total Rg	30.14 Å
Atom count	5919
Residues	758
Excluded volume	104170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gc7__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2gc7__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2gc7__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2gc7__assembly_4__model_1`	tetrameric （4）	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	Methylamine dehydrogenase heavy chain
Molecular weight formula_weight	42449.3 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M
Atom count atom_count	24910

QDAPEAETQAQETQGQAAARAAAADLAAGQDDEPRILEAPAPDARRVYVNDPAHFAAVTQQFVIDGEAGRVIGMIDGGFLPNPVVADDGSFIAHASTVFSRIARGERTDYVEVFDPVTLLPTADIELPDAPRFLVGTYPWMTSLTPDGKTLLFYQFSPAPAVGVVDLEGKAFKRMLDVPDCYHIFPTAPDTFFMHCRDGSLAKVAFGTEGTPEITHTEVFHPEDEFLINHPAYSQKAGRLVWPTYTGKIHQIDLSSGDAKFLPAVEALTEAERADGWRPGGWQQVAYHRALDRIYLLVDQRDEWRHKTASRFVVVLDAKTGERLAKFEMGHEIDSINVSQDEKPLLYALSTGDKTLYIHDAESGEELRSVNQLGHGPQVITTADMG

Entity 2 Entity 2 polymer

Description description	Methylamine dehydrogenase light chain
Molecular weight formula_weight	14210.7 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J,N

ADAPAGTDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS

Entity 3 Entity 3 polymer

Description description	Amicyanin
Molecular weight formula_weight	11505.2 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K,O

DKATIPSESPFAAAEVADGAIVVDIAKMKYETPELHVKVGDTVTWINREAMPHNVHFVAGVLGEAALKGPMMKKEQAYSLTFTEAGTYDYHCTPHPFMRGKVVVE

Entity 4 Entity 4 polymer

Description description	Cytochrome c-L
Molecular weight formula_weight	16274.9 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L,P

APQFFNIIDGSPLNFDDAMEEGRDTEAVKHFLETGENVYNEDPEILPEAEELYAGMCSGCHGHYAEGKIGPGLNDAYWTYPGNETDVGLFSTLYGGATGQMGPMWGSLTLDEMLRTMAWVRHLYTGDPKDASWLTDEQKAGFTPFQP

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 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	1234

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2gc7a_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family family	b.69.2.0 — automated matches

Domain ID domain_id	d2gc7b_
Class class	g — Small proteins
Fold Fold fold	g.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
Family Family family	g.21.1.1 — Methylamine dehydrogenase, L chain

Domain ID domain_id	d2gc7c_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d2gc7d_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d2gc7e_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family family	b.69.2.0 — automated matches

Domain ID domain_id	d2gc7f_
Class class	g — Small proteins
Fold Fold fold	g.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
Family Family family	g.21.1.1 — Methylamine dehydrogenase, L chain

Domain ID domain_id	d2gc7g_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d2gc7h_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d2gc7i_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family family	b.69.2.0 — automated matches

Domain ID domain_id	d2gc7j_
Class class	g — Small proteins
Fold Fold fold	g.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
Family Family family	g.21.1.1 — Methylamine dehydrogenase, L chain

Domain ID domain_id	d2gc7k_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d2gc7l_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d2gc7m_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family family	b.69.2.0 — automated matches

Domain ID domain_id	d2gc7n_
Class class	g — Small proteins
Fold Fold fold	g.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
Family Family family	g.21.1.1 — Methylamine dehydrogenase, L chain

Domain ID domain_id	d2gc7o_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d2gc7p_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

CATH v4.4 (16 domains)

Domain ID domain_id	2gc7A00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	2gc7B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

Domain ID domain_id	2gc7C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2gc7D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2gc7E00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	2gc7F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

Domain ID domain_id	2gc7G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2gc7H00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2gc7I00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	2gc7J00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

Domain ID domain_id	2gc7K00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2gc7L00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	2gc7M00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	2gc7N00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

Domain ID domain_id	2gc7O00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	2gc7P00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

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Unit-cell length a length_a	81.323 Å
Unit-cell length b length_b	189.127 Å
Unit-cell length c length_c	128.906 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	29.940 Å
R factor r_factor	—
R_work r_work	0.1710
R_free r_free	0.1980

Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans.

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

Methylamine dehydrogenase light chain

State in the Current Structure

Other States of the Same Protein in the Database

Amicyanin

State in the Current Structure

Other States of the Same Protein in the Database

Cytochrome c-L

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

2gc7__assembly_1__model_1

2gc7__assembly_1__model_1 | I(q)

2gc7__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

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

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (2)

Substrate reduced, copper free complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans.

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

Methylamine dehydrogenase light 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

Amicyanin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytochrome c-L

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

2gc7__assembly_1__model_1

2gc7__assembly_1__model_1 | I(q)

2gc7__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

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

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (2)