4IAV

G215S, A251G, T257A, D260G, T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris with N-Sulfamoyl-L-phenylalanine

PDB DOI: https://doi.org/10.2210/pdb4IAV/pdb

Classification: HYDROLASE
Organism(s): Thermoactinomyces vulgaris
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-12-07 Released: 2013-12-11
Deposition Author(s): Timofeev, V.I., Kuznetsov, S.A., Akparov, V.K., Kuranova, I.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.154
R-Value Work: 0.139
R-Value Observed: 0.140

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

G215S, A251G, T257A, D260G, T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris with N-Sulfamoyl-L-phenylalanine

Timofeev, V.I., Kuznetsov, S.A., Akparov, V.K., Kuranova, I.P.

To be published.

Macromolecule Content

Total Structure Weight: 38.62 kDa
Atom Count: 3,216
Modelled Residue Count: 323
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxypeptidase T	A	326	Thermoactinomyces vulgaris	Mutation(s): 5 Gene Names: cpt EC: 3.4.17.18
UniProt
Find proteins for P29068 (Thermoactinomyces vulgaris) Explore P29068 Go to UniProtKB: P29068
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29068
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXA Query on CXA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHENYLALANINE-N-SULFONAMIDE C₉ H₁₂ N₂ O₄ S PHGMHLLGXKQIDY-QMMMGPOBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain S [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain S [auth A]	H [auth A], I [auth A], S [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth A]	E [auth A] J [auth A] K [auth A] L [auth A] M [auth A] E [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], T [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth A] Interactions & Density Focus chain E [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain R [auth A] SDF format, chain U [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain R [auth A] MOL2 format, chain U [auth A]	D [auth A], F [auth A], G [auth A], R [auth A], U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth A] Focus chain U [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth A] Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.154
R-Value Work: 0.139
R-Value Observed: 0.140
Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.722	α = 90
b = 157.722	β = 90
c = 104.461	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	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: 2013-12-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Experimental preparation, Refinement description