3H9U | pdb_00003h9u

S-adenosyl homocysteine hydrolase (SAHH) from Trypanosoma brucei

PDB DOI: https://doi.org/10.2210/pdb3H9U/pdb

Deposited: 2009-04-30 Released: 2009-09-29
Deposition Author(s): Siponen, M.I., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kragh Nielsen, T., Kotenyova, T., Kotzsch, A., Moche, M., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Schueler, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.231 (Depositor), 0.290 (DCC)
R-Value Work:
0.196 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of S-adenosyl homocysteine hydrolase (SAHH) from Trypanosoma brucei

Siponen, M.I., Schutz, P., Arrowsmith, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 197.53 kDa
Atom Count: 14,413
Modeled Residue Count: 1,729
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	436	Trypanosoma brucei	Mutation(s): 0 Gene Names: SAHH, Tb11.01.1350 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q383X0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q383X0 Go to UniProtKB: Q383X0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q383X0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
ADN Query on ADN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain F [auth A]	F [auth A], H [auth B], K [auth C], N [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.231 (Depositor), 0.290 (DCC)
R-Value Work: 0.196 (Depositor)
R-Value Observed: 0.198 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.35	α = 90
b = 136.05	β = 99.32
c = 191.87	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-09-29

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description