3OF3 | pdb_00003of3

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb3OF3/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-08-13 Released: 2010-09-01
Deposition Author(s): Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.160 (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 2.2 of the entry. See complete history.

Literature

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae

Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 318.16 kDa
Atom Count: 24,255
Modeled Residue Count: 2,878
Deposited Residue Count: 2,892
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase deoD-type 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	241	Vibrio cholerae	Mutation(s): 0 Gene Names: deoD, deoD1, VC_2347 EC: 2.4.2.1
UniProt
Find proteins for Q9KPM0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KPM0 Go to UniProtKB: Q9KPM0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KPM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DIH Query on DIH Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain CA [auth I] SDF format, chain IA [auth L] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain W [auth F] SDF format, chain Y [auth G] SDF format, chain U [auth E] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain GA [auth K] SDF format, chain EA [auth J] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain IA [auth L] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain U [auth E] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth K] MOL2 format, chain EA [auth J] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain IA [auth L] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth G] mmCIF format, chain U [auth E] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth K] mmCIF format, chain EA [auth J]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one C₁₂ H₁₇ N₄ O₃ AFNHHLILYQEHKK-BDAKNGLRSA-O		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth G]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain DA [auth I] SDF format, chain HA [auth K] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Z [auth G] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain JA [auth L] SDF format, chain FA [auth J] MOL2 format, chain BA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain HA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain JA [auth L] MOL2 format, chain FA [auth J] mmCIF format, chain BA [auth H] mmCIF format, chain DA [auth I] mmCIF format, chain HA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain JA [auth L] mmCIF format, chain FA [auth J]	BA [auth H] DA [auth I] FA [auth J] HA [auth K] JA [auth L] BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.160 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.375	α = 90
b = 160.974	β = 90
c = 188.685	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-09-01

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2018-12-12
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 2.2: 2023-09-06
Changes: Data collection, Database references, Refinement description