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1nu9

Staphylocoagulase-Prethrombin-2 complex

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

Thrombin light and heavy chains

OrganismNot specified

UniProt P00734

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Staphylocoagulase × 1 （Q846V4） N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 MERCURY (II) ION × 2 IMIDAZOLE × 3 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Staphylocoagulase × 1 （Q846V4） N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 MERCURY (II) ION × 2 IMIDAZOLE × 3 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1cgl 1cgl 1jwt 1mh0 1mh0 3nxp 3sqe 3sqh 4h6t 4hzh 4hzh 4nzq

19 assemblies; showing the first 12

Homodimer
1abj 1awh 1awh 1hai 1jou 1jou 1jou 1ppb 1sfq 1sfq 1sg8 1sg8

74 assemblies; showing the first 12

Homotetramer
1sg8 1tq0 2a0q 2afq 2hnt 3jz1 3r3g 6p9u 6p9u 6p9u 6p9u

11 assemblies

Other homooligomers
2hpq

1 assemblies

Heteromeric or nucleic-acid complex
1a2c 1a3b 1a3e 1a46 1a4w 1a5g 1a61 1abi 1ad8 1ae8 1afe 1aht

460 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name THRB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–291； UniProt 332–622 Author chain D； PDBConstruct 1–291； UniProt 332–622

Staphylocoagulase

Staphylococcus aureus

UniProt Q846V4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Thrombin light and heavy chains × 1 （P00734） N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 MERCURY (II) ION × 2 IMIDAZOLE × 3 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Thrombin light and heavy chains × 1 （P00734） N-(sulfanylacetyl)-D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 MERCURY (II) ION × 2 IMIDAZOLE × 3 water × 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
1nu7 1nu7 1nu9 1nu9

4 assemblies

View Construct and Data Evidence
UniProt name Q846V4_STAAU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–281； UniProt 1–281 Author chain F； PDBConstruct 1–281； UniProt 1–281

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_id1nu9
Deposition date deposition_date2003-01-31
Structure title titleStaphylocoagulase-Prethrombin-2 complex
Keywords keywordsThrombin non-proteolytic activator, endocarditis, hydrolase-hydrolase inhibitor complex, protein binding; HYDROLASE/HYDROLASE INHIBITOR
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.

1nu9__assembly_1__model_1

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

Download this curve (.dat)

1nu9__assembly_1__model_1 | I(q)

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

1nu9__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）27.02 Å
Rg (electron density)26.19 Å
Total Rg26.87 Å
Atom count4730
Residues571
Excluded volume83930 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1nu9__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1nu9__assembly_2__model_1 dimeric （2） 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)

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1nu9a_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.2 — Eukaryotic proteases
Domain ID domain_idd1nu9c1
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.6 — Staphylocoagulase
Family Family familya.8.6.1 — Staphylocoagulase
Domain ID domain_idd1nu9c2
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.6 — Staphylocoagulase
Family Family familya.8.6.1 — Staphylocoagulase
Domain ID domain_idd1nu9d_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.2 — Eukaryotic proteases
Domain ID domain_idd1nu9f1
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.6 — Staphylocoagulase
Family Family familya.8.6.1 — Staphylocoagulase
Domain ID domain_idd1nu9f2
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.6 — Staphylocoagulase
Family Family familya.8.6.1 — Staphylocoagulase

CATH v4.4 (8 domains)

Domain ID domain_id1nu9A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1nu9A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1nu9C01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily750 — Staphylcoagulase, helix bundle domain 1
Domain ID domain_id1nu9C02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily760 — Staphylcoagulase, helix bundle, domain 2
Domain ID domain_id1nu9D01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1nu9D02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1nu9F01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily750 — Staphylcoagulase, helix bundle domain 1
Domain ID domain_id1nu9F02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily760 — Staphylcoagulase, helix bundle, domain 2
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7. Citations (1)