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Crystal structure of E. COLI ompf porin in complex with ertapenem

Analyse Crystal structure of E. COLI ompf porin in complex with ertapenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GCS
Type: protein
Length: 666 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein F
UniProt: P02931
Ligands: 1RG
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Outer membrane protein F	protein	333	4% helix, 61% strand	P02931

Ligands and binding sites

1RG · (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl) carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	983	0.71	0.75	68	empty
2	922	0.70	0.75	62	empty
3	277	0.49	0.73	38	empty
4	283	0.49	0.73	41	empty
5	67	0.44	0.80	11	empty

Interfaces

1 interface between chains.

A–B · 580 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4GCS · Crystal Structure of E. coli OmpF porin in complex with Ertapenem · the same entry in another collection · chain A against A, TM-score 1.00
P02931 · AlphaFold monomer V2.0 prediction for outer membrane porin F (P02931) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P02931
Elsewhere: RCSB PDB 4GCS · PDBe 4GCS · UniProt P02931

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