3GVP

Human SAHH-like domain of human adenosylhomocysteinase 3

PDB DOI: https://doi.org/10.2210/pdb3GVP/pdb

Deposited: 2009-03-31 Released: 2009-06-09
Deposition Author(s): Siponen, M.I., Wisniewska, M., 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., Kotenyova, T., Lehtio, L., Moche, M., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Schueler, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.226
R-Value Work: 0.182
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human S-adenosyl homocysteine hydrolase-like 2 protein crystal structure

Siponen, M.I., Wisniewska, M., 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., Kotenyova, T., Lehtio, L., Moche, M., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Schutz, P., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Schueler, H.

To be published.

Macromolecule Content

Total Structure Weight: 196.63 kDa
Atom Count: 14,173
Modelled Residue Count: 1,728
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase 3	A, B, C, D	435	Homo sapiens	Mutation(s): 0 Gene Names: AHCYL2, KIAA0828 EC: 3.3.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HN2 (Homo sapiens) Explore Q96HN2 Go to UniProtKB: Q96HN2
PHAROS: Q96HN2 GTEx: ENSG00000158467
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96HN2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.226
R-Value Work: 0.182
R-Value Observed: 0.182
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.188	α = 90
b = 164.188	β = 90
c = 184.614	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-06-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

3GVP

Human SAHH-like domain of human adenosylhomocysteinase 3

Human S-adenosyl homocysteine hydrolase-like 2 protein crystal structure

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)