5C54 | pdb_00005c54

Crystal structure of a novel N-acetylneuraminic acid lyase from Corynebacterium glutamicum

PDB DOI: https://doi.org/10.2210/pdb5C54/pdb

Classification: LYASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-06-19 Released: 2016-06-22
Deposition Author(s): Shen, Y., Zhou, J., Xie, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.194 (Depositor), 0.190 (DCC)
R-Value Work:
0.163 (Depositor), 0.170 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a novel N-acetylneuraminic acid lyase from Corynebacterium glutamicum

Shen, Y., Zhou, J., Xie, J.

To be published.

Macromolecule Content

Total Structure Weight: 262.99 kDa
Atom Count: 21,469
Modeled Residue Count: 2,473
Deposited Residue Count: 2,496
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase/N-acetylneuraminate lyase	A, B, C, D, E A, B, C, D, E, F, G, H	312	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: Cgl2646 EC: 4.1.3.3 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for Q8NMD2 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NMD2 Go to UniProtKB: Q8NMD2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NMD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain R [auth H] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] MOL2 format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H] mmCIF format, chain K [auth B]	I [auth A] J [auth B] K [auth B] L [auth C] M [auth D] I [auth A], J [auth B], K [auth B], L [auth C], M [auth D], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H]