1a5i

CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE)

Method: X-RAY DIFFRACTION D_max: 59.0 Å Quality: GOOD

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

PLASMINOGEN ACTIVATOR

Desmodus rotundus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 213–477	Fragment：UNP residues 213-477	0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；pH 9.0	Resolution 2.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	URT1_DESRO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–265； UniProt 213–477

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1a5i
Deposition date deposition_date	1998-02-17
Structure title title	CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE)
Keywords keywords	SERINE PROTEASE, FIBRINOLYTIC ENZYMES, PLASMINOGEN ACTIVATORS, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.45 Å
Radius of gyration Rg (electron density) rg_electron	17.49 Å
Forward intensity I(0) i0	30578600.00
Molecular weight molecular_weight	27976.0 kDa
Excluded volume excluded_volume	26787 Å³
Envelope volume envelope_volume	42839 Å³
Hydration-shell volume shell_volume	19799 Å³
Envelope diameter envelope_diameter	61.8 Å
Shell Rg shell_rg	24.47 Å
Envelope Rg envelope_rg	17.91 Å
Shape Rg shape_rg	17.48 Å
Total Rg total_rg	18.25 Å
Total atoms total_atoms	2108
Residues n_residues	265
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	59.0 Å
Rg (real space) rg_real	18.32 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	3.0580e+07
I(0) uncertainty (real space) i0_real_error	3.4480e+05
Rg (reciprocal space) rg_reciprocal	18.34 Å
I(0) (reciprocal space) i0_reciprocal	30580000.0000
Solution quality estimate total_estimate	0.8854
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.158
Kurtosis Kurtosis kurtosis	-0.359
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9444000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PLASMINOGEN ACTIVATOR
Molecular weight formula_weight	29716.6 kDa
EC 编号 ec_number	3.4.21.68
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	2141

TCGLRKYKEPQLHSTGGLFTDITSHPWQAAIFAQNRRSSGERFLCGGILISSCWVLTAAHCFQESYLPDQLKVVLGRTYRVKPGEEEQTFKVKKYIVHKEFDDDTYNNDIALLQLKSDSPQCAQESDSVRAICLPEANLQLPDWTECELSGYGKHKSSSPFYSEQLKEGHVRLYPSSRCAPKFLFNKTVTNNMLCAGDTRSGEIYPNVHDACQGDSGGPLVCMNDNHMTLLGIISWGVGCGEKDVPGVYTKVTNYLGWIRDNMHL

来源 Source

来源生物 organism	Desmodus rotundus
通用名 common_name	common vampire bat
NCBI Class编号 ncbi_taxonomy_id	9430
宿主生物 host_organism	Mesocricetus auratus

Entity 2 Entity 2 non-polymer

Description description	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide
Molecular weight formula_weight	395.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a5ia_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (2 domains)

Domain ID domain_id	1a5iA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1a5iA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (4)

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Unit-cell length a length_a	73.860 Å
Unit-cell length b length_b	73.860 Å
Unit-cell length c length_c	135.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	—

fit	/app/data/saxs_computation/a5/1a5i/1a5i.fit
pddf	/app/data/pr_computation/a5/1a5i/1a5i.pr.out
profile	/app/data/saxs_computation/a5/1a5i/1a5i.dat