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Structure of gfcc (ymcb), protein encoded by the E. COLI group 4 capsule operon

Analyse Structure of gfcc (ymcb), protein encoded by the E. COLI group 4 capsule operon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P42
Type: protein
Length: 914 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Predicted protein
UniProt: B7UN63
Ligands: SO4
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Predicted protein	protein	234	30% helix, 24% strand	B7UN63
B	Predicted protein	protein	225	28% helix, 26% strand	B7UN63
C	Predicted protein	protein	226	27% helix, 25% strand	B7UN63
D	Predicted protein	protein	229	28% helix, 24% strand	B7UN63

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains B, D

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	823	0.87	0.89	91	empty
2	557	0.75	0.82	56	empty
3	218	0.74	0.89	39	empty
4	547	0.73	0.81	44	empty
5	245	0.70	0.86	35	empty

Interfaces

5 interfaces between chains.

A–B · 1290 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1271 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1253 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 553 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 267 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

3P42 · Structure of GfcC (YmcB), protein encoded by the E. coli group 4 capsule operon · the same entry in another collection · chain C against C, 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 B7UN63
Elsewhere: RCSB PDB 3P42 · PDBe 3P42 · UniProt B7UN63

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