MolNFT v1 · #121213 · protein

Mamb-ctd mutant - D247A

5HOK · Magnetosome protein mamb: “Mamb-ctd mutant - D247A”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.65). MolNFT v1 #121213 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HOK
Type: protein
Length: 332 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Magnetosome protein mamb
UniProt: W6KHH6
Ligands: MG
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Magnetosome protein mamb	protein	83	37% helix, 39% strand	W6KHH6
B, D	Magnetosome protein mamb	protein	84	37% helix, 39% strand	W6KHH6
C	Magnetosome protein mamb	protein	81	38% helix, 40% strand	W6KHH6

Ligands and binding sites

MG · Magnesium ion · metal · chains B

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

Pockets

2 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	478	0.65	0.77	46	empty
2	305	0.60	0.78	43	empty

Interfaces

3 interfaces between chains.

B–C · 717 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 536 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 237 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5HOK · MamB-CTD mutant - D247A · the same entry in another collection · chain A against A, TM-score 1.00
W6KHH6 · AlphaFold monomer V2.0 prediction for magnetosome protein mamb (W6KHH6) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 W6KHH6
Elsewhere: RCSB PDB 5HOK · PDBe 5HOK · UniProt W6KHH6

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