9IVN | pdb_00009ivn

Crystal structure of KRED mutant-Y199A/N149L

PDB DOI: https://doi.org/10.2210/pdb9IVN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-07-24 Released: 2025-07-30
Deposition Author(s): Xu, H., Zhang, Z., Zhang, Y., Xu, Y., Zhang, L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.206 (Depositor), 0.211 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: in silico
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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

Chemoenzymatic synthesis of key squalamine intermediate by engineered ketoreductase mutants from Novosphingobium aromaticivorans

Zhang, Z., Xu, H., Kong, P., Cao, J., Li, S., Zhang, Y., Xu, Y., Zhang, L.

To be published.

Macromolecule Content

Total Structure Weight: 220.99 kDa
Atom Count: 15,639
Modeled Residue Count: 2,066
Deposited Residue Count: 2,072
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A B C D [auth F] E [auth G] A, B, C, D [auth F], E [auth G], F [auth H], G [auth D], H [auth E]	259	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 2 Gene Names: Saro_3543
UniProt
Find proteins for A4XEP2 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XEP2 Go to UniProtKB: A4XEP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XEP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain W [auth G] SDF format, chain S [auth F] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain FA [auth E] SDF format, chain CA [auth D] MOL2 format, chain Z [auth H] MOL2 format, chain W [auth G] MOL2 format, chain S [auth F] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain CA [auth D] mmCIF format, chain Z [auth H] mmCIF format, chain W [auth G] mmCIF format, chain S [auth F] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain CA [auth D]	CA [auth D] FA [auth E] I [auth A] M [auth B] P [auth C] CA [auth D], FA [auth E], I [auth A], M [auth B], P [auth C], S [auth F], W [auth G], Z [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain CA [auth D] Focus chain FA [auth E] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth F] Focus chain W [auth G] Focus chain Z [auth H] Interactions & Density Focus chain CA [auth D] Focus chain FA [auth E] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth F] Focus chain W [auth G] Focus chain Z [auth H]
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth G] SDF format, chain T [auth F] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain GA [auth E] SDF format, chain DA [auth D] SDF format, chain AA [auth H] MOL2 format, chain X [auth G] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain DA [auth D] MOL2 format, chain AA [auth H] mmCIF format, chain X [auth G] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain DA [auth D] mmCIF format, chain AA [auth H]	AA [auth H] DA [auth D] GA [auth E] J [auth A] N [auth B] AA [auth H], DA [auth D], GA [auth E], J [auth A], N [auth B], Q [auth C], T [auth F], X [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth F] Focus chain X [auth G] Interactions & Density Focus chain AA [auth H] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth F] Focus chain X [auth G]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain O [auth B] SDF format, chain BA [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain O [auth B] MOL2 format, chain BA [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain O [auth B] mmCIF format, chain BA [auth H]	BA [auth H], O [auth B], Y [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth H] Focus chain O [auth B] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain O [auth B] Focus chain Y [auth G]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
DMS (Subject of Investigation/LOI) Query on DMS Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain JA [auth E] SDF format, chain IA [auth E] SDF format, chain EA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain EA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain EA [auth D]	EA [auth D], IA [auth E], JA [auth E], K [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A] Interactions & Density Focus chain EA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain K [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain R [auth C] SDF format, chain HA [auth E] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain R [auth C] MOL2 format, chain HA [auth E] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain R [auth C] mmCIF format, chain HA [auth E]	HA [auth E], R [auth C], U [auth F], V [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Focus chain R [auth C] Focus chain U [auth F] Focus chain V [auth F] Interactions & Density Focus chain HA [auth E] Focus chain R [auth C] Focus chain U [auth F] Focus chain V [auth F]