7F35 | pdb_00007f35

Crystal structure of anti S-gatifloxacin antibody Fab fragment in complex with S-gatifloxacin

PDB DOI: https://doi.org/10.2210/pdb7F35/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2021-06-15 Released: 2021-12-29
Deposition Author(s): Wang, L.T., Jiao, W.Y., Shen, X., Lei, H.T.
Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Conformational adaptability determining antibody recognition to distomer: structure analysis of enantioselective antibody against chiral drug gatifloxacin

Wang, L.T., Xie, W., Jiao, W.Y., Zhang, C., Li, X., Xu, Z., Huang, X., Lei, H.T., Shen, X.

(2021) RSC Adv 11: 39534-39544

DOI: https://doi.org/10.1039/D1RA07143B

Macromolecule Content

Total Structure Weight: 145.7 kDa
Atom Count: 9,706
Modelled Residue Count: 1,229
Deposited Residue Count: 1,308
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab fragment light chain	A, C, E	218	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab fragment heavy chain	B, D, F	218	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GFN (Subject of Investigation/LOI) Query on GFN Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain Q [auth C] SDF format, chain G [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain G [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain G [auth A]	DA [auth E], G [auth A], Q [auth C]	1-cyclopropyl-6-fluoro-8-methoxy-7-[(3S)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid C₁₉ H₂₂ F N₃ O₄ XUBOMFCQGDBHNK-JTQLQIEISA-N		Interactions Focus chain DA [auth E] Focus chain G [auth A] Focus chain Q [auth C] Interactions & Density Focus chain DA [auth E] Focus chain G [auth A] Focus chain Q [auth C]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain HA [auth F] MOL2 format, chain HA [auth F] mmCIF format, chain HA [auth F]	HA [auth F]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain HA [auth F] Interactions & Density Focus chain HA [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Z [auth D] SDF format, chain GA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain GA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain K [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain GA [auth F]	EA [auth F] FA [auth F] GA [auth F] K [auth B] R [auth C] EA [auth F], FA [auth F], GA [auth F], K [auth B], R [auth C], S [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain K [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain K [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	T [auth C], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain T [auth C] Focus chain U [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C]	H [auth A] I [auth A] IA [auth F] JA [auth F] L [auth B] H [auth A], I [auth A], IA [auth F], JA [auth F], L [auth B], M [auth B], N [auth B], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain Y [auth C]	Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain X [auth C] SDF format, chain J [auth A] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] MOL2 format, chain J [auth A] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C] mmCIF format, chain J [auth A] mmCIF format, chain W [auth C]	AA [auth D] BA [auth D] CA [auth D] J [auth A] O [auth B] AA [auth D], BA [auth D], CA [auth D], J [auth A], O [auth B], P [auth B], W [auth C], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C]