3MTG

Crystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein

PDB DOI: https://doi.org/10.2210/pdb3MTG/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-04-30 Released: 2010-05-26
Deposition Author(s): Wisniewska, M., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nordlund, P., Nyman, T., Persson, C., Schutz, P., Thorsell, A.G., Tresaugues, L., van der Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Schuler, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.249
R-Value Work: 0.203
R-Value Observed: 0.204

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 human S-adenosyl homocysteine hydrolase-like 1 protein

Wisniewska, M., Siponen, M.I., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nordlund, P., Nyman, T., Persson, C., Schutz, P., Thorsell, A.G., Tresaugues, L., van der Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Schuler, H.

To be published.

Macromolecule Content

Total Structure Weight: 100.28 kDa
Atom Count: 6,792
Modelled Residue Count: 853
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative adenosylhomocysteinase 2	A, B	444	Homo sapiens	Mutation(s): 1 Gene Names: AHCYL1, DCAL, Irbit, XPVKONA EC: 3.3.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43865 (Homo sapiens) Explore O43865 Go to UniProtKB: O43865
PHAROS: O43865 GTEx: ENSG00000168710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43865
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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.249
R-Value Work: 0.203
R-Value Observed: 0.204
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.24	α = 90
b = 68.6	β = 115.27
c = 90.37	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BALBES	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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3MTG

Crystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein

Crystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)