3RU4 | pdb_00003ru4

Crystal structure of the Bowman-Birk serine protease inhibitor BTCI in complex with trypsin and chymotrypsin

PDB DOI: https://doi.org/10.2210/pdb3RU4/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Bos taurus, Vigna unguiculata
Mutation(s): No

Deposited: 2011-05-04 Released: 2012-08-29
Deposition Author(s): Esteves, G.F., Santos, C.R., Ventura, M.M., Barbosa, J.A.R.G., Freitas, S.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the Bowman-Birk serine protease inhibitor BTCI in complex with trypsin and chymotrypsin

Esteves, G.F., Teles, R.C.L., Cavalcante, N.S., Neves, D., Ventura, M.M., Barbosa, J.A.R.G., Freitas, S.M.

To be published.

Macromolecule Content

Total Structure Weight: 57.1 kDa
Atom Count: 4,732
Modeled Residue Count: 522
Deposited Residue Count: 522
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A [auth T]	223	Bos taurus	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760 Go to UniProtKB: P00760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bowman-Birk type seed trypsin and chymotrypsin inhibitor	B	61	Vigna unguiculata	Mutation(s): 0
UniProt
Find proteins for P17734 (Vigna unguiculata) Explore P17734 Go to UniProtKB: P17734
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsinogen A	C	11	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsinogen A	D	131	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsinogen A	E	96	Bos taurus	Mutation(s): 0 EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766 Go to UniProtKB: P00766
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00766
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain R [auth T] SDF format, chain Y [auth D] MOL2 format, chain R [auth T] MOL2 format, chain Y [auth D] mmCIF format, chain R [auth T] mmCIF format, chain Y [auth D]	R [auth T], Y [auth D]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain R [auth T] Focus chain Y [auth D] Interactions & Density Focus chain R [auth T] Focus chain Y [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain L [auth T] SDF format, chain M [auth T] SDF format, chain N [auth T] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain L [auth T] MOL2 format, chain M [auth T] MOL2 format, chain N [auth T] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain L [auth T] mmCIF format, chain M [auth T] mmCIF format, chain N [auth T] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	AA [auth E] L [auth T] M [auth T] N [auth T] T [auth B] AA [auth E], L [auth T], M [auth T], N [auth T], T [auth B], U [auth B], V [auth D], W [auth D], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain L [auth T] Focus chain M [auth T] Focus chain N [auth T] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain L [auth T] Focus chain M [auth T] Focus chain N [auth T] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth D] Focus chain W [auth D] Focus chain Z [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth T] SDF format, chain H [auth T] SDF format, chain I [auth T] SDF format, chain J [auth T] SDF format, chain K [auth T] SDF format, chain S [auth B] MOL2 format, chain G [auth T] MOL2 format, chain H [auth T] MOL2 format, chain I [auth T] MOL2 format, chain J [auth T] MOL2 format, chain K [auth T] MOL2 format, chain S [auth B] mmCIF format, chain G [auth T] mmCIF format, chain H [auth T] mmCIF format, chain I [auth T] mmCIF format, chain J [auth T] mmCIF format, chain K [auth T] mmCIF format, chain S [auth B]	G [auth T] H [auth T] I [auth T] J [auth T] K [auth T] G [auth T], H [auth T], I [auth T], J [auth T], K [auth T], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth T] Focus chain H [auth T] Focus chain I [auth T] Focus chain J [auth T] Focus chain K [auth T] Focus chain S [auth B] Interactions & Density Focus chain G [auth T] Focus chain H [auth T] Focus chain I [auth T] Focus chain J [auth T] Focus chain K [auth T] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain O [auth T] SDF format, chain P [auth T] SDF format, chain Q [auth T] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain O [auth T] MOL2 format, chain P [auth T] MOL2 format, chain Q [auth T] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain O [auth T] mmCIF format, chain P [auth T] mmCIF format, chain Q [auth T] mmCIF format, chain X [auth D]	BA [auth E] CA [auth E] O [auth T] P [auth T] Q [auth T] BA [auth E], CA [auth E], O [auth T], P [auth T], Q [auth T], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain O [auth T] Focus chain P [auth T] Focus chain Q [auth T] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain O [auth T] Focus chain P [auth T] Focus chain Q [auth T] Focus chain X [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth T] MOL2 format, chain F [auth T] mmCIF format, chain F [auth T]	F [auth T]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth T] Interactions & Density Focus chain F [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.477	α = 67.28
b = 54.571	β = 71.04
c = 69.286	γ = 73.55

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary