3QQM

Crystal structure of a Putative amino-acid aminotransferase (NP_104211.1) from Mesorhizobium loti at 2.30 A resolution

PDB DOI: https://doi.org/10.2210/pdb3QQM/pdb

Classification: TRANSFERASE
Organism(s): Mesorhizobium loti
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-02-15 Released: 2011-03-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.241
R-Value Work: 0.193
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a Putative amino-acid aminotransferase (NP_104211.1) from Mesorhizobium loti at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 204.99 kDa
Atom Count: 14,246
Modelled Residue Count: 1,686
Deposited Residue Count: 1,768
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mlr3007 protein	A, B, C, D, E A, B, C, D, E, F, G, H	221	Mesorhizobium loti	Mutation(s): 0 Gene Names: mlr3007
UniProt
Find proteins for Q98H69 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98H69 Go to UniProtKB: Q98H69
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q98H69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AC [auth F] SDF format, chain BA [auth B] SDF format, chain BC [auth F] SDF format, chain EC [auth G] SDF format, chain FC [auth G] SDF format, chain GC [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain LB [auth E] SDF format, chain LC [auth H] SDF format, chain MA [auth C] SDF format, chain MB [auth E] SDF format, chain MC [auth H] SDF format, chain NC [auth H] SDF format, chain OC [auth H] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZB [auth F] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain BC [auth F] MOL2 format, chain EC [auth G] MOL2 format, chain FC [auth G] MOL2 format, chain GC [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain LB [auth E] MOL2 format, chain LC [auth H] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth E] MOL2 format, chain MC [auth H] MOL2 format, chain NC [auth H] MOL2 format, chain OC [auth H] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZB [auth F]	AA [auth B] AC [auth F] BA [auth B] BC [auth F] EC [auth G] AA [auth B], AC [auth F], BA [auth B], BC [auth F], EC [auth G], FC [auth G], GC [auth G], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], LA [auth C], LB [auth E], LC [auth H], MA [auth C], MB [auth E], MC [auth H], NC [auth H], OC [auth H], UA [auth D], VA [auth D], WA [auth D], Y [auth B], Z [auth B], ZB [auth F]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AC [auth F] Focus chain BA [auth B] Focus chain BC [auth F] Focus chain EC [auth G] Focus chain FC [auth G] Focus chain GC [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain LC [auth H] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain MC [auth H] Focus chain NC [auth H] Focus chain OC [auth H] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth F] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth F] Focus chain BA [auth B] Focus chain BC [auth F] Focus chain EC [auth G] Focus chain FC [auth G] Focus chain GC [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain LC [auth H] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain MC [auth H] Focus chain NC [auth H] Focus chain OC [auth H] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth F]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain CA [auth B] MOL2 format, chain CA [auth B]	CA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Interactions & Density Focus chain CA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain CC [auth F] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain DC [auth F] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain IA [auth B] SDF format, chain IB [auth D] SDF format, chain IC [auth G] SDF format, chain JB [auth D] SDF format, chain JC [auth G] SDF format, chain KB [auth D] SDF format, chain KC [auth G] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain QB [auth E] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain RB [auth E] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain SB [auth E] SDF format, chain SC [auth H] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain TB [auth E] SDF format, chain TC [auth H] SDF format, chain U [auth A] SDF format, chain UB [auth E] SDF format, chain UC [auth H] SDF format, chain V [auth A] SDF format, chain VB [auth E] SDF format, chain W [auth A] SDF format, chain WB [auth E] SDF format, chain X [auth A] SDF format, chain XB [auth E] SDF format, chain YB [auth E] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain CC [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain DC [auth F] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain IC [auth G] MOL2 format, chain JB [auth D] MOL2 format, chain JC [auth G] MOL2 format, chain KB [auth D] MOL2 format, chain KC [auth G] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth E] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth E] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth E] MOL2 format, chain SC [auth H] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth E] MOL2 format, chain TC [auth H] MOL2 format, chain U [auth A] MOL2 format, chain UB [auth E] MOL2 format, chain UC [auth H] MOL2 format, chain V [auth A] MOL2 format, chain VB [auth E] MOL2 format, chain W [auth A] MOL2 format, chain WB [auth E] MOL2 format, chain X [auth A] MOL2 format, chain XB [auth E] MOL2 format, chain YB [auth E] MOL2 format, chain ZA [auth D]	AB [auth D] BB [auth D] CB [auth D] CC [auth F] DA [auth B] AB [auth D], BB [auth D], CB [auth D], CC [auth F], DA [auth B], DB [auth D], DC [auth F], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], HB [auth D], IA [auth B], IB [auth D], IC [auth G], JB [auth D], JC [auth G], KB [auth D], KC [auth G], NA [auth C], OA [auth C], PA [auth C], Q [auth A], QA [auth C], QB [auth E], R [auth A], RA [auth C], RB [auth E], S [auth A], SA [auth C], SB [auth E], SC [auth H], T [auth A], TA [auth C], TB [auth E], TC [auth H], U [auth A], UB [auth E], UC [auth H], V [auth A], VB [auth E], W [auth A], WB [auth E], X [auth A], XB [auth E], YB [auth E], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain IC [auth G] Focus chain JB [auth D] Focus chain JC [auth G] Focus chain KB [auth D] Focus chain KC [auth G] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain SC [auth H] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth E] Focus chain TC [auth H] Focus chain U [auth A] Focus chain UB [auth E] Focus chain UC [auth H] Focus chain V [auth A] Focus chain VB [auth E] Focus chain W [auth A] Focus chain WB [auth E] Focus chain X [auth A] Focus chain XB [auth E] Focus chain YB [auth E] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain IC [auth G] Focus chain JB [auth D] Focus chain JC [auth G] Focus chain KB [auth D] Focus chain KC [auth G] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain SC [auth H] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth E] Focus chain TC [auth H] Focus chain U [auth A] Focus chain UB [auth E] Focus chain UC [auth H] Focus chain V [auth A] Focus chain VB [auth E] Focus chain W [auth A] Focus chain WB [auth E] Focus chain X [auth A] Focus chain XB [auth E] Focus chain YB [auth E] Focus chain ZA [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HC [auth G] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NB [auth E] SDF format, chain O [auth A] SDF format, chain OB [auth E] SDF format, chain P [auth A] SDF format, chain PB [auth E] SDF format, chain PC [auth H] SDF format, chain QC [auth H] SDF format, chain RC [auth H] SDF format, chain XA [auth D] SDF format, chain YA [auth D] MOL2 format, chain HC [auth G] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth E] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth E] MOL2 format, chain PC [auth H] MOL2 format, chain QC [auth H] MOL2 format, chain RC [auth H] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D]	HC [auth G] L [auth A] M [auth A] N [auth A] NB [auth E] HC [auth G], L [auth A], M [auth A], N [auth A], NB [auth E], O [auth A], OB [auth E], P [auth A], PB [auth E], PC [auth H], QC [auth H], RC [auth H], XA [auth D], YA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HC [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NB [auth E] Focus chain O [auth A] Focus chain OB [auth E] Focus chain P [auth A] Focus chain PB [auth E] Focus chain PC [auth H] Focus chain QC [auth H] Focus chain RC [auth H] Focus chain XA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain HC [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NB [auth E] Focus chain O [auth A] Focus chain OB [auth E] Focus chain P [auth A] Focus chain PB [auth E] Focus chain PC [auth H] Focus chain QC [auth H] Focus chain RC [auth H] Focus chain XA [auth D] Focus chain YA [auth D]

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