SAXSdb — 1a86

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

MMP-8

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	N-benzyl-N~2~-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-alpha-asparagine × 1 CALCIUM ION × 2 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MM08_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 105–262

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	1a86
Deposition date deposition_date	1998-04-03
Structure title title	MMP8 WITH MALONIC AND ASPARTIC ACID BASED INHIBITOR
Keywords keywords	COLLAGENASE, MATRIX METALLOPROTEINASE, MALONIC ACID, MMP8, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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.

1a86__assembly_1__model_1

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

Download this curve (.dat)

1a86__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1a86__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.80 Å
Rg (electron density)	14.47 Å
Total Rg	15.63 Å
Atom count	1282
Residues	158
Excluded volume	22186 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1a86__assembly_1__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	MMP-8
Molecular weight formula_weight	17612.1 kDa
EC 编号 ec_number	3.4.24.34
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1282

NPKWERTNLTYRIRNYTPQLSEAEVERAIKDAFELWSVASPLIFTRISQGEADINIAFYQRDHGDNSPFDGPNGILAHAFQPGQGIGGDAHFDAEETWTNTSANYNLFLVAAHEFGHSLGLAHSSDPGALMYPNYAFRETSNYSLPQDDIDGIQAIYG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 2 Entity 2 non-polymer

Description description	N-benzyl-N~2~-[(2R)-2-(hydroxycarbamoyl)-4-methylpentanoyl]-L-alpha-asparagine
Molecular weight formula_weight	379.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a86a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.11 — Matrix metalloproteases, catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id	1a86A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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Unit-cell length a length_a	33.140 Å
Unit-cell length b length_b	69.430 Å
Unit-cell length c length_c	72.620 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	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

MMP8 WITH MALONIC AND ASPARTIC ACID BASED INHIBITOR

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

MMP-8

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

1a86__assembly_1__model_1

1a86__assembly_1__model_1 | I(q)

1a86__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

MMP8 WITH MALONIC AND ASPARTIC ACID BASED INHIBITOR

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

MMP-8

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

1a86__assembly_1__model_1

1a86__assembly_1__model_1 | I(q)

1a86__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)