8JT0

Dihydrofolate reductase-like enzyme from Leptospira interrogans with additional NADP+

PDB DOI: https://doi.org/10.2210/pdb8JT0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leptospira interrogans serovar Pomona
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-20 Released: 2024-06-26
Deposition Author(s): Wangkanont, K.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.247
R-Value Work: 0.206
R-Value Observed: 0.208

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Dihydrofolate reductase-like enzyme from Leptospira interrogans with additional NADP+

Wangkanont, K.

To be published.

Macromolecule Content

Total Structure Weight: 240.53 kDa
Atom Count: 17,041
Modelled Residue Count: 1,972
Deposited Residue Count: 2,030
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase family protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	203	Leptospira interrogans serovar Pomona	Mutation(s): 0 Gene Names: IQB77_11460
UniProt
Find proteins for A0AA40WBR8 (Leptospira interrogans serovar Pomona) Explore A0AA40WBR8 Go to UniProtKB: A0AA40WBR8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AA40WBR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain CB [auth H] SDF format, chain GB [auth I] SDF format, chain HA [auth E] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain OB [auth J] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain UA [auth G] SDF format, chain Z [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain GB [auth I] MOL2 format, chain HA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain OB [auth J] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain UA [auth G] MOL2 format, chain Z [auth D]	CB [auth H] GB [auth I] HA [auth E] M [auth A] MA [auth F] CB [auth H], GB [auth I], HA [auth E], M [auth A], MA [auth F], OB [auth J], P [auth B], T [auth C], UA [auth G], Z [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain CB [auth H] Focus chain GB [auth I] Focus chain HA [auth E] Focus chain M [auth A] Focus chain MA [auth F] Focus chain OB [auth J] Focus chain P [auth B] Focus chain T [auth C] Focus chain UA [auth G] Focus chain Z [auth D] Interactions & Density Focus chain CB [auth H] Focus chain GB [auth I] Focus chain HA [auth E] Focus chain M [auth A] Focus chain MA [auth F] Focus chain OB [auth J] Focus chain P [auth B] Focus chain T [auth C] Focus chain UA [auth G] Focus chain Z [auth D]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain BB [auth H] SDF format, chain EB [auth I] SDF format, chain GA [auth E] SDF format, chain K [auth A] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain LB [auth J] SDF format, chain MB [auth J] SDF format, chain NB [auth J] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain SA [auth G] SDF format, chain X [auth D] MOL2 format, chain AB [auth H] MOL2 format, chain BB [auth H] MOL2 format, chain EB [auth I] MOL2 format, chain GA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain LB [auth J] MOL2 format, chain MB [auth J] MOL2 format, chain NB [auth J] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain X [auth D]	AB [auth H] BB [auth H] EB [auth I] GA [auth E] K [auth A] AB [auth H], BB [auth H], EB [auth I], GA [auth E], K [auth A], KA [auth F], L [auth A], LA [auth F], LB [auth J], MB [auth J], NB [auth J], O [auth B], S [auth C], SA [auth G], X [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain BB [auth H] Focus chain EB [auth I] Focus chain GA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain LB [auth J] Focus chain MB [auth J] Focus chain NB [auth J] Focus chain O [auth B] Focus chain S [auth C] Focus chain SA [auth G] Focus chain X [auth D] Interactions & Density Focus chain AB [auth H] Focus chain BB [auth H] Focus chain EB [auth I] Focus chain GA [auth E] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain LA [auth F] Focus chain LB [auth J] Focus chain MB [auth J] Focus chain NB [auth J] Focus chain O [auth B] Focus chain S [auth C] Focus chain SA [auth G] Focus chain X [auth D]
SO4 Query on SO4 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 DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain HB [auth I] SDF format, chain IA [auth E] SDF format, chain IB [auth I] SDF format, chain JA [auth E] SDF format, chain JB [auth I] SDF format, chain KB [auth I] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain PB [auth J] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain QB [auth J] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain RB [auth J] SDF format, chain SB [auth J] SDF format, chain TB [auth J] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain VA [auth G] SDF format, chain W [auth C] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain HB [auth I] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth I] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth I] MOL2 format, chain KB [auth I] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain PB [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain QB [auth J] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain RB [auth J] MOL2 format, chain SB [auth J] MOL2 format, chain TB [auth J] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] DB [auth H] AA [auth D], BA [auth D], CA [auth D], DA [auth D], DB [auth H], EA [auth D], FA [auth D], HB [auth I], IA [auth E], IB [auth I], JA [auth E], JB [auth I], KB [auth I], N [auth A], NA [auth F], OA [auth F], PA [auth F], PB [auth J], Q [auth B], QA [auth F], QB [auth J], R [auth B], RA [auth F], RB [auth J], SB [auth J], TB [auth J], U [auth C], V [auth C], VA [auth G], W [auth C], WA [auth G], XA [auth G], YA [auth G], ZA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain HB [auth I] Focus chain IA [auth E] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain JB [auth I] Focus chain KB [auth I] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain PB [auth J] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain QB [auth J] Focus chain R [auth B] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain HB [auth I] Focus chain IA [auth E] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain JB [auth I] Focus chain KB [auth I] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain PB [auth J] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain QB [auth J] Focus chain R [auth B] Focus chain RA [auth F] Focus chain RB [auth J] Focus chain SB [auth J] Focus chain TB [auth J] Focus chain U [auth C] Focus chain V [auth C] Focus chain VA [auth G] Focus chain W [auth C] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain FB [auth I] SDF format, chain TA [auth G] SDF format, chain Y [auth D] MOL2 format, chain FB [auth I] MOL2 format, chain TA [auth G] MOL2 format, chain Y [auth D]	FB [auth I], TA [auth G], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain FB [auth I] Focus chain TA [auth G] Focus chain Y [auth D] Interactions & Density Focus chain FB [auth I] Focus chain TA [auth G] Focus chain Y [auth D]