8OQ2 | pdb_00008oq2

Binding of NADP to a formate dehydrogenase from Starkeya novella.

PDB DOI: https://doi.org/10.2210/pdb8OQ2/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Ancylobacter novellus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-04-10 Released: 2024-04-24
Deposition Author(s): Partipilo, M., Whittaker, J.J., Pontillo, N., Guskov, A., Slotboom, D.J.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.275 (Depositor), 0.251 (DCC)
R-Value Work:
0.237 (Depositor)

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.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7QZ1

Literature

Binding of NADP to a formate dehydrogenase from Starkeya novella.

Partipilo, M., Whittaker, J.J., Pontillo, N., Coenradij, J., Herrmann, A., Guskov, A., Slotboom, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 257.18 kDa
Atom Count: 18,219
Modeled Residue Count: 2,285
Deposited Residue Count: 2,286
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B, C, D, E A, B, C, D, E, F	381	Ancylobacter novellus	Mutation(s): 4 Gene Names: Snov_3272 EC: 1.17.1.9
UniProt
Find proteins for D7A8L2 (Ancylobacter novellus (strain ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM 12100 / NBRC 12443 / NCIMB 10456)) Explore D7A8L2 Go to UniProtKB: D7A8L2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D7A8L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain P [auth C] SDF format, chain Z [auth F] SDF format, chain Y [auth E] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth D]	G [auth A] H [auth B] P [auth C] X [auth D] Y [auth E] G [auth A], H [auth B], P [auth C], X [auth D], Y [auth E], Z [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain P [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	I [auth B] J [auth B] K [auth B] L [auth B] M [auth B] I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]