6I34

Crystal structure of Neanderthal glycine decarboxylase (P-protein)

PDB DOI: https://doi.org/10.2210/pdb6I34/pdb

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

Deposited: 2018-11-05 Released: 2019-11-20
Deposition Author(s): Van Laer, B., Kapp, U., Leonard, G., Mueller-Dieckmann, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.243
R-Value Work: 0.216
R-Value Observed: 0.218

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural insights in human glycine decarboxylase and comparison with the Neanderthal variant

Van Laer, B., Kapp, U., Signor, L., Leonard, G., Mueller-Dieckmann, C.

To be published.

Macromolecule Content

Total Structure Weight: 440.85 kDa
Atom Count: 31,302
Modelled Residue Count: 3,813
Deposited Residue Count: 3,936
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neanderthal Glycine decarboxylase	A, B, C, D	984	Homo sapiens neanderthalensis	Mutation(s): 0 EC: 1.4.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23378 (Homo sapiens) Explore P23378 Go to UniProtKB: P23378
PHAROS: P23378 GTEx: ENSG00000178445
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23378
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain Z [auth D]	E [auth A], L [auth B], Q [auth C], Z [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain Z [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	I [auth A], P [auth B], U [auth C], V [auth C], Y [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain I [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain W [auth C] SDF format, chain CA [auth D] SDF format, chain K [auth A] SDF format, chain X [auth C] MOL2 format, chain J [auth A] MOL2 format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain X [auth C] mmCIF format, chain J [auth A] mmCIF format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain X [auth C]	CA [auth D], J [auth A], K [auth A], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain W [auth C] Focus chain X [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain AA [auth D] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	AA [auth D] BA [auth D] F [auth A] G [auth A] H [auth A] AA [auth D], BA [auth D], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C]