4GCP: E. coli OmpF porin

Crystal Structure of E. coli OmpF porin in complex with Ampicillin. Determined by X-ray diffraction at 1.98 Å resolution. Released 19 Dec 2012.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Escherichia coli
Chains: 2
Atoms: 5,469
Mol. weight: 75.04 kDa
Ligands: AIC
Released: 19 Dec 2012

Explore 4GCP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GCP contains 9 α-helices and 44 β-strands across 2 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: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	9-23	15	1
β-strand	31	1	2
β-strand	36-37	2	1
β-strand	40-52	13	1
β-strand	55-66	12	1
β-strand	80-90	11	1
β-strand	94-102	9	1
α-helix	106-109	4
β-strand	132-142	11	1
α-helix	143-146	4
β-strand	151-158	8	1
β-strand	161	1	3
α-helix	166-168	3
β-strand	170	1	3
β-strand	173-182	10	1
β-strand	185-195	11	1
α-helix	196-197	2
α-helix	198-201	4
β-strand	205	1	1
β-strand	210-222	13	1
β-strand	225-242	18	1
β-strand	247-263	17	1
β-strand	269-283	15	1
β-strand	287-302	16	1
β-strand	307-316	10	1
β-strand	329	1	2
β-strand	331-339	9	1

Chain B: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	9-23	15	4
β-strand	31	1	5
β-strand	36-37	2	4
β-strand	40-50	11	4
β-strand	55-66	12	4
β-strand	80-90	11	4
β-strand	94-102	9	4
α-helix	106-109	4
β-strand	132-141	10	4
α-helix	143-146	4
β-strand	151-158	8	4
β-strand	161	1	6
β-strand	170	1	6
β-strand	173-182	10	4
β-strand	185-195	11	4
α-helix	196-197	2
α-helix	198-201	4
β-strand	205	1	4
β-strand	210-222	13	4
β-strand	225-242	18	4
β-strand	247-263	17	4
β-strand	269-283	15	4
β-strand	287-302	16	4
β-strand	307-316	10	4
β-strand	329	1	5
β-strand	331-339	9	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein F	A, B	protein	341	Escherichia coli	P02931 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4GCP_1 Outer membrane protein F (chains A, B)
GAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYG
QWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFG
GDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSIS
YEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATP
ITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGA
TYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF

Ligands and cofactors

ID	Name	Formula	Copies
AIC	(2S,5R,6R)-6-{[(2R)-2-amino-2-phenylethanoyl]amino}-3,3-dimethyl-7-oxo-4-thia-1…	C16 H19 N3 O4 S	2

Primary citation

The Binding of Antibiotics in OmpF Porin. Ziervogel, B.K., Roux, B. Structure (2013) 21:76-87. DOI 10.1016/j.str.2012.10.014 · PubMed

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
6ZHV 1.95 Å, Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
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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