4XQ2

Ensemble refinement of cystathione gamma lyase (CalE6) D7G from Micromonospora echinospora

PDB DOI: https://doi.org/10.2210/pdb4XQ2/pdb

Classification: LYASE
Organism(s): Micromonospora echinospora
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-01-18 Released: 2015-04-15
Deposition Author(s): Wang, F., Yennamalli, R.M., Singh, S., Tan, K., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.183
R-Value Work: 0.143
R-Value Observed: 0.145

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora

Yennamalli, R.M., Tan, K., Wang, F., Bigelow, L., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Joachimiak, A., Kharel, M.K., Singh, S., Thorson, J.S., Phillips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 335.2 kDa
Atom Count: 24,344
Modelled Residue Count: 3,018
Deposited Residue Count: 3,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalE6	A, B, C, D, E A, B, C, D, E, F, G, H	384	Micromonospora echinospora	Mutation(s): 1 Gene Names: calE6
UniProt
Find proteins for Q8KNG3 (Micromonospora echinospora) Explore Q8KNG3 Go to UniProtKB: Q8KNG3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KNG3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain CB [auth H] SDF format, chain I [auth A] SDF format, chain IA [auth E] SDF format, chain MA [auth F] SDF format, chain O [auth B] SDF format, chain VA [auth G] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain VA [auth G] MOL2 format, chain X [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain MA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain VA [auth G] mmCIF format, chain X [auth C]	CA [auth D] CB [auth H] I [auth A] IA [auth E] MA [auth F] CA [auth D], CB [auth H], I [auth A], IA [auth E], MA [auth F], O [auth B], VA [auth G], X [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain CB [auth H] Focus chain I [auth A] Focus chain IA [auth E] Focus chain MA [auth F] Focus chain O [auth B] Focus chain VA [auth G] Focus chain X [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain EB [auth H] SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain Y [auth C] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain FA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth G] mmCIF format, chain ZA [auth G]	DA [auth D] DB [auth H] EA [auth D] EB [auth H] FA [auth D] DA [auth D], DB [auth H], EA [auth D], EB [auth H], FA [auth D], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], NA [auth F], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], RA [auth F], S [auth B], SA [auth F], T [auth B], U [auth B], V [auth B], WA [auth G], XA [auth G], Y [auth C], YA [auth G], ZA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain ZA [auth G]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain TA [auth F] SDF format, chain Z [auth C] MOL2 format, chain AB [auth G] MOL2 format, chain TA [auth F] MOL2 format, chain Z [auth C] mmCIF format, chain AB [auth G] mmCIF format, chain TA [auth F] mmCIF format, chain Z [auth C]	AB [auth G], TA [auth F], Z [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain TA [auth F] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain BB [auth G] SDF format, chain FB [auth H] SDF format, chain GA [auth D] SDF format, chain GB [auth H] SDF format, chain HA [auth D] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain UA [auth F] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain FB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain HA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain UA [auth F] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth G] mmCIF format, chain FB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain HA [auth D] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain UA [auth F] mmCIF format, chain W [auth B]	AA [auth C] BA [auth C] BB [auth G] FB [auth H] GA [auth D] AA [auth C], BA [auth C], BB [auth G], FB [auth H], GA [auth D], GB [auth H], HA [auth D], LA [auth E], M [auth A], N [auth A], UA [auth F], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain UA [auth F] Focus chain W [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET