6M0Q

Hydroxylamine oxidoreductase from Nitrosomonas europaea

PDB DOI: https://doi.org/10.2210/pdb6M0Q/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitrosomonas europaea
Mutation(s): No

Deposited: 2020-02-22 Released: 2021-03-10
Deposition Author(s): Fujiwara, T., Fujimoto, Z., Nishigaya, Y., Yamazaki, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.200
R-Value Work: 0.163
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Enhancement of the activity of hydroxylamine oxidoreductase by juglone, plant secondary metabolite.

Fujiwara, T., Fujimoto, Z., Nishigaya, Y., Yamazaki, T.

To be published.

Macromolecule Content

Total Structure Weight: 476.55 kDa
Atom Count: 31,763
Modelled Residue Count: 3,408
Deposited Residue Count: 3,966
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aerobic hydroxylamine oxidoreductase	A, C, E, G, I A, C, E, G, I, K	570	Nitrosomonas europaea	Mutation(s): 0
UniProt
Find proteins for Q50925 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q50925 Go to UniProtKB: Q50925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50925
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	B, D, F, H, J B, D, F, H, J, L	91	Nitrosomonas europaea	Mutation(s): 0
UniProt
Find proteins for Q82V11 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82V11 Go to UniProtKB: Q82V11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q82V11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ISW Query on ISW Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain MB [auth I] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain AB [auth G] SDF format, chain BB [auth G] MOL2 format, chain FA [auth C] MOL2 format, chain MB [auth I] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G]	AB [auth G] BB [auth G] FA [auth C] MB [auth I] T [auth A] AB [auth G], BB [auth G], FA [auth C], MB [auth I], T [auth A], U [auth A]	{3,3'-[(9S)-8,13-diethenyl-3,7,12,17-tetramethyl-9,10-dihydroporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~]dipropanoato(2-)}iron C₃₄ H₃₄ Fe N₄ O₄ QSWMAEGFLATCMU-JMAPEOGHSA-L		Interactions Focus chain AB [auth G] Focus chain BB [auth G] Focus chain FA [auth C] Focus chain MB [auth I] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth G] Focus chain FA [auth C] Focus chain MB [auth I] Focus chain T [auth A] Focus chain U [auth A]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain FB [auth I] SDF format, chain GB [auth I] SDF format, chain IB [auth I] SDF format, chain JA [auth E] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QB [auth K] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SB [auth K] SDF format, chain TA [auth G] SDF format, chain TB [auth K] SDF format, chain UA [auth G] SDF format, chain VB [auth K] SDF format, chain WB [auth K] SDF format, chain XA [auth G] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain AA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain HB [auth I] SDF format, chain JB [auth I] SDF format, chain KA [auth E] SDF format, chain KB [auth I] SDF format, chain LA [auth E] SDF format, chain LB [auth I] SDF format, chain M [auth A] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain RB [auth K] SDF format, chain UB [auth K] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain FB [auth I] MOL2 format, chain GB [auth I] MOL2 format, chain IB [auth I] MOL2 format, chain JA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth K] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth K] MOL2 format, chain TA [auth G] MOL2 format, chain TB [auth K] MOL2 format, chain UA [auth G] MOL2 format, chain VB [auth K] MOL2 format, chain WB [auth K] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain HB [auth I] MOL2 format, chain JB [auth I] MOL2 format, chain KA [auth E] MOL2 format, chain KB [auth I] MOL2 format, chain LA [auth E] MOL2 format, chain LB [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain RB [auth K] MOL2 format, chain UB [auth K] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FB [auth I], GB [auth I], HB [auth I], IB [auth I], JA [auth E], JB [auth I], KA [auth E], KB [auth I], LA [auth E], LB [auth I], M [auth A], MA [auth E], N [auth A], NA [auth E], O [auth A], OA [auth E], P [auth A], PA [auth E], Q [auth A], QB [auth K], R [auth A], RB [auth K], S [auth A], SB [auth K], TA [auth G], TB [auth K], UA [auth G], UB [auth K], VA [auth G], VB [auth K], WA [auth G], WB [auth K], XA [auth G], Y [auth C], YA [auth G], Z [auth C], ZA [auth G]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FB [auth I] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain JB [auth I] Focus chain KA [auth E] Focus chain KB [auth I] Focus chain LA [auth E] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QB [auth K] Focus chain R [auth A] Focus chain RB [auth K] Focus chain S [auth A] Focus chain SB [auth K] Focus chain TA [auth G] Focus chain TB [auth K] Focus chain UA [auth G] Focus chain UB [auth K] Focus chain VA [auth G] Focus chain VB [auth K] Focus chain WA [auth G] Focus chain WB [auth K] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FB [auth I] Focus chain GB [auth I] Focus chain HB [auth I] Focus chain IB [auth I] Focus chain JA [auth E] Focus chain JB [auth I] Focus chain KA [auth E] Focus chain KB [auth I] Focus chain LA [auth E] Focus chain LB [auth I] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QB [auth K] Focus chain R [auth A] Focus chain RB [auth K] Focus chain S [auth A] Focus chain SB [auth K] Focus chain TA [auth G] Focus chain TB [auth K] Focus chain UA [auth G] Focus chain UB [auth K] Focus chain VA [auth G] Focus chain VB [auth K] Focus chain WA [auth G] Focus chain WB [auth K] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain Z [auth C] Focus chain ZA [auth G]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain SA [auth E] SDF format, chain ZB [auth K] SDF format, chain X [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain SA [auth E] MOL2 format, chain ZB [auth K] MOL2 format, chain X [auth A]	IA [auth C], SA [auth E], X [auth A], ZB [auth K]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain SA [auth E] Focus chain X [auth A] Focus chain ZB [auth K] Interactions & Density Focus chain IA [auth C] Focus chain SA [auth E] Focus chain X [auth A] Focus chain ZB [auth K]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain DB [auth G] SDF format, chain HA [auth C] SDF format, chain NB [auth I] SDF format, chain OB [auth I] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain EB [auth G] SDF format, chain W [auth A] MOL2 format, chain DB [auth G] MOL2 format, chain HA [auth C] MOL2 format, chain NB [auth I] MOL2 format, chain OB [auth I] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain EB [auth G] MOL2 format, chain W [auth A]	DB [auth G] EB [auth G] HA [auth C] NB [auth I] OB [auth I] DB [auth G], EB [auth G], HA [auth C], NB [auth I], OB [auth I], QA [auth E], RA [auth E], W [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain DB [auth G] Focus chain EB [auth G] Focus chain HA [auth C] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain W [auth A] Interactions & Density Focus chain DB [auth G] Focus chain EB [auth G] Focus chain HA [auth C] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain W [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain CB [auth G] SDF format, chain GA [auth C] SDF format, chain PB [auth J] SDF format, chain XB [auth K] SDF format, chain YB [auth K] MOL2 format, chain V [auth A] MOL2 format, chain CB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain PB [auth J] MOL2 format, chain XB [auth K] MOL2 format, chain YB [auth K]	CB [auth G] GA [auth C] PB [auth J] V [auth A] XB [auth K] CB [auth G], GA [auth C], PB [auth J], V [auth A], XB [auth K], YB [auth K]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CB [auth G] Focus chain GA [auth C] Focus chain PB [auth J] Focus chain V [auth A] Focus chain XB [auth K] Focus chain YB [auth K] Interactions & Density Focus chain CB [auth G] Focus chain GA [auth C] Focus chain PB [auth J] Focus chain V [auth A] Focus chain XB [auth K] Focus chain YB [auth K]