MolNFT v1 · #124238 · protein

Crystal structure of microcin immunity protein mccf from bacillus anthracis in complex with mcc

5K99 · Microcin C7 self-immunity protein mccf: “Crystal structure of microcin immunity protein mccf from bacillus anthracis in complex with mcc”. X-ray diffraction, 1 ligand (AMP), 4 pockets (best druggability 0.80). MolNFT v1 #124238 on…

PDB: 5K99
Type: protein
Length: 681 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microcin C7 self-immunity protein mccf; Microcin C
UniProt: Q81RT8
Ligands: AMP
Pockets: 4 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Microcin C7 self-immunity protein mccf	protein	336	31% helix, 22% strand	Q81RT8
C, D	Microcin C	protein	6	0% helix, 0% strand	—
B	Microcin C7 self-immunity protein mccf	protein	333	32% helix, 23% strand	Q81RT8

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.80	0.82	109	AMP
2	92	0.40	0.77	22	empty
3	54	0.33	0.77	17	empty
4	57	0.27	0.73	13	empty

Interfaces

6 interfaces between chains.

A–B · 1864 Å² buried · 47 hydrogen bonds · protein-protein
B–D · 306 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 303 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 100 Å² buried · 2 hydrogen bonds · protein-protein
C–B · 93 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified, 2 covalent (engineered, covalent ligand, nonstandard).

Compared structures

5K99 · Crystal structure of microcin immunity protein MccF from Bacillus anthracis in complex… · the same entry in another collection · 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 Q81RT8
Elsewhere: RCSB PDB 5K99 · PDBe 5K99 · UniProt Q81RT8

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