2VD6

Human adenylosuccinate lyase in complex with its substrate N6-(1,2- Dicarboxyethyl)-AMP, and its products AMP and fumarate.

PDB DOI: https://doi.org/10.2210/pdb2VD6/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-09-30 Released: 2007-10-23
Deposition Author(s): Stenmark, P., Moche, M., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-schiavone, L., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Nilsson, M., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Thorsell, A.G., Tresaugues, L., van den Berg, S., Weigelt, J., Welin, M., Nordlund, P., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.229
R-Value Work: 0.192
R-Value Observed: 0.194

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Human Adenylosuccinate Lyase in Complex with its Substrate N6-(1,2-Dicarboxyethyl)-AMP, and its Products AMP and Fumarate.

Stenmark, P., Moche, M., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Nilsson, M., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Nordlund, P.

To be published.

Macromolecule Content

Total Structure Weight: 231.33 kDa
Atom Count: 15,817
Modelled Residue Count: 1,841
Deposited Residue Count: 2,012
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENYLOSUCCINATE LYASE	A, B, C, D	503	Homo sapiens	Mutation(s): 0 EC: 4.3.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for P30566 (Homo sapiens) Explore P30566 Go to UniProtKB: P30566
PHAROS: P30566 GTEx: ENSG00000239900
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30566
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2SA Query on 2SA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain S [auth D] MOL2 format, chain J [auth B] MOL2 format, chain S [auth D] mmCIF format, chain J [auth B] mmCIF format, chain S [auth D]	J [auth B], S [auth D]	2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC ACID C₁₄ H₁₈ N₅ O₁₁ P OFBHPPMPBOJXRT-VWJPMABRSA-N		Interactions Focus chain J [auth B] Focus chain S [auth D] Interactions & Density Focus chain J [auth B] Focus chain S [auth D]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain E [auth A] MOL2 format, chain O [auth C] MOL2 format, chain E [auth A] mmCIF format, chain O [auth C] mmCIF format, chain E [auth A]	E [auth A], O [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain O [auth C]
FUM Query on FUM Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain P [auth C]	F [auth A], P [auth C]	FUMARIC ACID C₄ H₄ O₄ VZCYOOQTPOCHFL-OWOJBTEDSA-N		Interactions Focus chain F [auth A] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	G [auth A], K [auth B], L [auth B], Q [auth C], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain T [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain I [auth A] SDF format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain I [auth A] MOL2 format, chain R [auth C] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain I [auth A] mmCIF format, chain R [auth C]	H [auth A] I [auth A] M [auth B] N [auth B] R [auth C] H [auth A], I [auth A], M [auth B], N [auth B], R [auth C], U [auth D], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.229
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.3	α = 90
b = 128.1	β = 90
c = 190.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

Holmberg-schiavone, L.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2012-07-18
Changes: Other
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Other
Version 2.1: 2023-12-13
Changes: Refinement description