1TK2 | pdb_00001tk2

Crystal Structure of the Complex formed between Alkaline Proteinase Savinase and Gramicidin S at 1.5A Resolution

PDB DOI: https://doi.org/10.2210/pdb1TK2/pdb

Classification: HYDROLASE/ANTIBIOTIC
Organism(s): Lederbergia lenta, Brevibacillus brevis
Mutation(s): No

Deposited: 2004-06-08 Released: 2004-06-22
Deposition Author(s): Bhatt, V.S., Kaur, P., Klupsch, S., Betzel, C., Brenner, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.189 (Depositor)
R-Value Work:
0.169 (Depositor)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the Complex Formed between Alkaline Proteinase Savinase and Gramicidin S at 1.5A Resolution.

Bhatt, V.S., Kaur, P., Klupsch, S., Betzel, C., Brenner, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 27.96 kDa
Atom Count: 2,155
Modeled Residue Count: 279
Deposited Residue Count: 279
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUBTILISIN SAVINASE	A	269	Lederbergia lenta	Mutation(s): 0 EC: 3.4.21.62
UniProt
Find proteins for P29600 (Lederbergia lenta) Explore P29600 Go to UniProtKB: P29600
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29600
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GRAMICIDIN S	B	10	Brevibacillus brevis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DPN Query on DPN	B	D-PEPTIDE LINKING	C₉ H₁₁ N O₂		--
ORN Query on ORN	B	L-PEPTIDE LINKING	C₅ H₁₂ N₂ O₂		ALA

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000219 Query on PRD_000219	B	GRAMICIDIN S	Cyclic peptide / Antibiotic		Interactions Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.189 (Depositor)
R-Value Work: 0.169 (Depositor)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.25	α = 90
b = 73.34	β = 90
c = 40.89	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-06-22
Type: Initial release
Version 1.1: 2011-06-14
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-07-27
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
Version 1.4: 2012-12-12
Changes: Other
Version 1.5: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description