7TAV

Crystal Structure of the PBP2_YvgL_like protein Lmo1041 from Listeria monocytogene

PDB DOI: https://doi.org/10.2210/pdb7TAV/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-21 Released: 2021-12-29
Deposition Author(s): Kim, Y., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.251
R-Value Work: 0.213
R-Value Observed: 0.215

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the PBP2_YvgL_like protein Lmo1041 from Listeria monocytogenes

Kim, Y., Maltseva, N., Grimshaw, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 153.75 kDa
Atom Count: 10,464
Modelled Residue Count: 1,351
Deposited Residue Count: 1,398
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdate ABC transporter substrate-binding protein	A, B, C, D, E A, B, C, D, E, F	233	Listeria monocytogenes	Mutation(s): 0 Gene Names: modA
UniProt
Find proteins for A0A5D5LL32 (Listeria monocytogenes) Explore A0A5D5LL32 Go to UniProtKB: A0A5D5LL32
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5D5LL32
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain GA [auth F] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	BA [auth E] GA [auth F] L [auth A] N [auth B] T [auth C] BA [auth E], GA [auth F], L [auth A], N [auth B], T [auth C], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain GA [auth F] Focus chain L [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain GA [auth F] Focus chain L [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain W [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain G [auth A] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] mmCIF format, chain CA [auth F] mmCIF format, chain G [auth A]	CA [auth F], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain G [auth A] Interactions & Density Focus chain CA [auth F] Focus chain G [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain M [auth B] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain M [auth B] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain M [auth B]	AA [auth E] DA [auth F] EA [auth F] FA [auth F] H [auth A] AA [auth E], DA [auth F], EA [auth F], FA [auth F], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], X [auth E], Y [auth E], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]