Research workbench

Fima type V pilus from P.GINGIVALIS

Analyse Fima type V pilus from P.GINGIVALIS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KMF
Type: protein
Length: 1,011 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major fimbrium subunit fima type-1
UniProt: B2RH54
Pockets: 5 · best druggability 0.67

Structure

electron microscopy · 3 distinct chains · 5% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major fimbrium subunit fima type-1	protein	316	6% helix, 31% strand	B2RH54
B, C	Major fimbrium subunit fima type-1	protein	337	4% helix, 34% strand	B2RH54
D	Major fimbrium subunit fima type-1	protein	21	0% helix, 76% strand	B2RH54

Pockets

5 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	342	0.67	0.82	42	empty
2	308	0.67	0.82	38	empty
3	53	0.36	0.79	18	empty
4	58	0.35	0.79	13	empty
5	54	0.28	0.74	12	empty

Interfaces

4 interfaces between chains.

B–C · 2461 Å² buried · 48 hydrogen bonds · protein-protein
A–B · 2409 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2038 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 12 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6KMF · FimA type V pilus from P.gingivalis · the same entry in another collection · chain D against D, TM-score 1.00
B2RH54 · AlphaFold monomer V2.0 prediction for major fimbrium subunit fima type-1 (B2RH54) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 B2RH54
Elsewhere: RCSB PDB 6KMF · PDBe 6KMF · UniProt B2RH54

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