3D67

Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI) in complex with 2-guanidino-ethyl-mercaptosuccinic acid (GEMSA)

PDB DOI: https://doi.org/10.2210/pdb3D67/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2008-05-19 Released: 2008-07-01
Deposition Author(s): Brondijk, T.H.C., Huizinga, E.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.252
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 149.34 kDa
Atom Count: 9,940
Modelled Residue Count: 1,203
Deposited Residue Count: 1,272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxypeptidase B2	A, B, C	424	Homo sapiens	Mutation(s): 0 Gene Names: CPB2 EC: 3.4.17.20
UniProt & NIH Common Fund Data Resources
Find proteins for Q96IY4 (Homo sapiens) Explore Q96IY4 Go to UniProtKB: Q96IY4
PHAROS: Q96IY4 GTEx: ENSG00000080618
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96IY4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GEM Query on GEM Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C]	I [auth A], O [auth B], T [auth C]	(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID C₇ H₁₃ N₃ O₄ S VKVCLXDFOQQABP-BYPYZUCNSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C]	D [auth A] E [auth A] F [auth A] G [auth A] J [auth B] D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B], P [auth C], Q [auth C], R [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C]	H [auth A], N [auth B], S [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain S [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
GEM	PDBBind: 3D67	Ki: 1.10e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.252
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.05	α = 90
b = 161.05	β = 90
c = 138.99	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-01

Deposition Author(s):

Brondijk, T.H.C.

Huizinga, E.G.

Revision History (Full details and data files)

Version 1.0: 2008-07-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-06-20
Changes: Data collection, Source and taxonomy
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3D67

Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI) in complex with 2-guanidino-ethyl-mercaptosuccinic acid (GEMSA)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)