6ZHV: Outer membrane porin F

Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic. Determined by X-ray diffraction at 1.95 Å resolution. Released 5 May 2021.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Escherichia coli (strain K12)
Chains: 3
Atoms: 8,226
Mol. weight: 120.28 kDa
Ligands: MG, QLB
Released: 5 May 2021

Explore 6ZHV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZHV contains 13 α-helices and 69 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	23-28	6	4
β-strand	31-45	15	4
β-strand	53	1	5
β-strand	58-59	2	4
β-strand	62-74	13	4
β-strand	77-88	12	4
β-strand	102-112	11	4
β-strand	116-124	9	4
α-helix	128-131	4
α-helix	132-134	3
β-strand	154-163	10	4
α-helix	165-168	4
β-strand	173-180	8	4
α-helix	181-182	2
β-strand	183	1	6
β-strand	192	1	6
β-strand	195-204	10	4
β-strand	207-217	11	4
α-helix	218-219	2
α-helix	220-224	5
β-strand	227	1	4
β-strand	232-244	13	4
β-strand	247-264	18	4
β-strand	269-285	17	4
β-strand	291-305	15	4
β-strand	309-326	18	4
β-strand	329-338	10	4
β-strand	351	1	5
β-strand	353-361	9	4

Chain B: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	23-28	6	1
β-strand	31-45	15	1
β-strand	53	1	2
β-strand	58-59	2	1
β-strand	62-74	13	1
β-strand	77-88	12	1
β-strand	102-112	11	1
β-strand	116-124	9	1
α-helix	128-131	4
β-strand	154-163	10	1
β-strand	173-180	8	1
β-strand	183	1	3
β-strand	192	1	3
β-strand	195-204	10	1
β-strand	207-217	11	1
α-helix	218-219	2
α-helix	220-223	4
β-strand	227	1	1
β-strand	232-244	13	1
β-strand	247-264	18	1
β-strand	269-285	17	1
β-strand	291-305	15	1
β-strand	309-324	16	1
β-strand	329-338	10	1
β-strand	351	1	2
β-strand	353-361	9	1

Chain C: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	24-28	5	7
β-strand	31-46	16	7
β-strand	53	1	8
β-strand	58-59	2	7
β-strand	62-74	13	7
β-strand	77-88	12	7
β-strand	102-112	11	7
β-strand	116-124	9	7
α-helix	128-131	4
β-strand	154-163	10	7
β-strand	173-180	8	7
α-helix	181-182	2
β-strand	183	1	9
β-strand	192	1	9
β-strand	195-204	10	7
β-strand	207-217	11	7
α-helix	218-219	2
α-helix	220-223	4
β-strand	227	1	7
β-strand	232-244	13	7
β-strand	247-264	18	7
β-strand	269-285	17	7
β-strand	291-305	15	7
β-strand	309-324	16	7
β-strand	329-338	10	7
β-strand	351	1	8
β-strand	353-361	9	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane porin F	A, B, C	protein	362	Escherichia coli (strain K12)	P02931 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6ZHV_1 Outer membrane porin F (chains A, B, C)
MMKRNILAVIVPALLVAGTANAAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDM
TYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDY
GRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYL
GKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGL
KYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKS
KAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVY
QF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
QLB	2-[2-(2-octoxyethoxy)ethoxy]ethanol	C14 H30 O4	7

Water and common crystallization additives (NA) are not listed.

Primary citation

Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic. Sousa, C.F., Morais-Cabral, J., Gameiro, P. To be published.

Other PDB entries of the same protein (UniProt P02931 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZFG 1.59 Å, Structure of OMPF PORIN
4GCS 1.87 Å, Crystal Structure of E. coli OmpF porin in complex with Ertapenem
3POQ 1.9 Å, Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, small…
4LSF 1.9 Å, Ion selectivity of OmpF soaked in 0.1M KBr
4GCP 1.98 Å, Crystal Structure of E. coli OmpF porin in complex with Ampicillin
3POX 2.0 Å, Crystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1
6ZHP 2.05 Å, Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
4LSI 2.09 Å, Ion selectivity of OmpF porin soaked in 0.3M KBr
4LSE 2.1 Å, Ion selectivity of OmpF porin soaked in 0.2M NaBr
1HXX 2.2 Å, Ompf porin mutant Y106F
4GCQ 2.2 Å, Crystal Structure of E. coli OmpF porin in complex with Carbenicillin
4LSH 2.2 Å, Ion selectivity of OmpF porin soaked in 0.2M KBr

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