2ZHP | pdb_00002zhp

Crystal structure of bleomycin-binding protein from Streptoalloteichus hindustanus complexed with bleomycin derivative

PDB DOI: https://doi.org/10.2210/pdb2ZHP/pdb

Classification: ANTIBIOTIC INHIBITOR
Organism(s): Streptoalloteichus hindustanus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-06 Released: 2009-02-17
Deposition Author(s): Okumura, H., Miyazaki, I., Simizu, S., Osada, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.216 (Depositor), 0.216 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-Affinity Relationship Study of Bleomycins and Shble protein Using a Chemical Array

Miyazaki, I., Okumura, H., Simizu, S., Takahashi, Y., Kanoh, N., Nonomura, Y., Osada, H.

To be published.

Macromolecule Content

Total Structure Weight: 30.84 kDa
Atom Count: 2,202
Modeled Residue Count: 231
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bleomycin resistance protein	A, B	124	Streptoalloteichus hindustanus	Mutation(s): 0
UniProt
Find proteins for P17493 (Streptoalloteichus hindustanus) Explore P17493 Go to UniProtKB: P17493
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17493
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BY6 Query on BY6 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	[(2S,3R,4R,5S,6S)-2-[(3R,4R,5R,6R)-2-[(1R,2S)-2-[[6-amino-2-[(1S)-3-amino-1-[(2,3-diamino-3-oxopropyl)amino]-3-oxopropyl]-5-methylpyrimidine-4-carbonyl]amino]-3-[[(2S,3R,4R)-5-[[(2R,3S)-1-[2-[4-[4-[3-[4-(3-aminopropylamino)butylamino]propylcarbamoyl]-1,3-thiazol-2-yl]-1,3-thiazol-2-yl]ethylamino]-3-hydroxy-1-oxobutan-2-yl]amino]-3-hydroxy-4-methyl-5-oxopentan-2-yl]amino]-1-(3H-imidazol-4-yl)-3-oxopropoxy]-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl]oxy-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl] carbamate C₆₀ H₉₆ N₂₀ O₂₁ S₂ FOUFFVYWFNBHHH-YNGSZULRSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.216 (Depositor), 0.216 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.992	α = 90
b = 53.868	β = 90
c = 125.498	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-02-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations