6A89 | pdb_00006a89

Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution

PDB DOI: https://doi.org/10.2210/pdb6A89/pdb

Classification: IMMUNE SYSTEM
Organism(s): Camelus dromedarius
Mutation(s): No

Deposited: 2018-07-06 Released: 2018-07-25
Deposition Author(s): Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.249 (Depositor), 0.254 (DCC)
R-Value Work:
0.191 (Depositor), 0.200 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution

Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 74.94 kDa
Atom Count: 5,559
Modeled Residue Count: 668
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan recognition protein 1	A, B, C, D	167	Camelus dromedarius	Mutation(s): 0
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12 Go to UniProtKB: Q9GK12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9GK12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
API Query on API Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	2,6-DIAMINOPIMELIC ACID C₇ H₁₄ N₂ O₄ GMKMEZVLHJARHF-SYDPRGILSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
RIB Query on RIB Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	alpha-D-ribofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-AIHAYLRMSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.249 (Depositor), 0.254 (DCC)
R-Value Work: 0.191 (Depositor), 0.200 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.5	α = 90
b = 101.37	β = 90
c = 163.04	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-07-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-07-25
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Structure summary
Version 3.1: 2023-11-22
Changes: Refinement description