6N91 | pdb_00006n91

Crystal Structure of Adenosine Deaminase from Vibrio cholerae Complexed with Pentostatin (Deoxycoformycin)

PDB DOI: https://doi.org/10.2210/pdb6N91/pdb

Classification: HYDROLASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-11-30 Released: 2018-12-19
Deposition Author(s): Maltseva, N., Kim, Y., Endres, M., Welk, L., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.174 (Depositor), 0.175 (DCC)
R-Value Work:
0.154 (Depositor), 0.155 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Adenosine Deaminase from Vibrio cholerae Complexed with Pentostatin (Deoxycoformycin) (CASP target)

Maltseva, N., Kim, Y., Endres, M., Welk, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 76.53 kDa
Atom Count: 5,990
Modeled Residue Count: 668
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase	A, B	340	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: add, VC_2751 EC: 3.5.4.4
UniProt
Find proteins for Q9KNI7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KNI7 Go to UniProtKB: Q9KNI7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KNI7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCF Query on DCF Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	2'-DEOXYCOFORMYCIN C₁₁ H₁₆ N₄ O₄ FPVKHBSQESCIEP-JQCXWYLXSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
CXS Query on CXS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth B]	E [auth A], L [auth B], R [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain H [auth A]	H [auth A], Q [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A]	I [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A], M [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.174 (Depositor), 0.175 (DCC)
R-Value Work: 0.154 (Depositor), 0.155 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.906	α = 90
b = 134.906	β = 90
c = 136.144	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-12-19
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description