3G8F

Crystal structure of the complex formed between a group II phospholipase A2 and designed peptide inhibitor carbobenzoxy-dehydro-val-ala-arg-ser at 1.2 A resolution

PDB DOI: https://doi.org/10.2210/pdb3G8F/pdb
Entry: 3G8F supersedes: 1TJQ

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Daboia russelii russelii
Mutation(s): No

Deposited: 2009-02-12 Released: 2009-03-10
Deposition Author(s): Singh, N., Kaur, P., Prem Kumar, R., Somvanshi, R.K., Perbandt, M., Betzel, C., Dey, S., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 ?
R-Value Free:
0.210 (Depositor), 0.220 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the Complex Formed between a Group II Phospholipase A2 and Designed Peptide Inhibitor Carbobenzoxy-Dehydro-Val-Ala-Arg-Ser at 1.2 A Resolution

Singh, N., Kaur, P., Prem Kumar, R., Somvanshi, R.K., Perband, M., Betzel, C., Dey, S., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 14.5 kDa
Atom Count: 1,198
Modelled Residue Count: 126
Deposited Residue Count: 126
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 VRV-PL-VIIIa	A	121	Daboia russelii russelii	Mutation(s): 0 EC: 3.1.1.4
UniProt
Find proteins for P59071 (Daboia russelii) Explore P59071 Go to UniProtKB: P59071
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59071
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHQ VAL ALA ARG SER peptide	B	5	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000339 Query on PRD_000339	B	CARBOBENZOXY-DEHYDRO-VAL-ALA-ARG-SER	Peptide-like / Inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 ?
R-Value Free: 0.210 (Depositor), 0.220 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( ? )	Angle ( ? )
a = 52.561	α = 90
b = 52.561	β = 90
c = 47.883	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

This entry supersedes: 1TJQ

Revision History (Full details and data files)

Version 1.0: 2009-03-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary