MolNFT v1 · #151243 · protein

Mamm ctd E289D - cadmium form

6HHS · Magnetosome protein mamm, cation efflux protein family: “Mamm ctd E289D - cadmium form”. X-ray diffraction, 2 ligands (CD, SO4), 12 pockets (best druggability 0.69). MolNFT v1 #151243 on GenesisL1: 3D structure, binding sites and…

PDB: 6HHS
Type: protein
Length: 587 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Magnetosome protein mamm, cation efflux protein family; Probable C-terminal region of…
UniProt: Q6NE57
Ligands: CD, SO4
Pockets: 12 · best druggability 0.69

Structure

x-ray diffraction · 8 distinct chains · 38% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Magnetosome protein mamm, cation efflux protein family	protein	83	37% helix, 36% strand	Q6NE57
B	Magnetosome protein mamm, cation efflux protein family	protein	88	34% helix, 35% strand	Q6NE57
C	Magnetosome protein mamm, cation efflux protein family	protein	81	38% helix, 37% strand	Q6NE57
D	Magnetosome protein mamm, cation efflux protein family	protein	83	37% helix, 36% strand	Q6NE57
E	Magnetosome protein mamm, cation efflux protein family	protein	82	38% helix, 37% strand	Q6NE57
F	Magnetosome protein mamm, cation efflux protein family	protein	82	38% helix, 35% strand	Q6NE57
G	Magnetosome protein mamm, cation efflux protein family	protein	80	39% helix, 38% strand	Q6NE57
M	Probable C-terminal region of mamm ctd E289D - cadmium form	protein	8	63% helix, 0% strand	—

Ligands and binding sites

CD · Cadmium ion · metal · 12 copies · chains A, C, D, B, G, E, F
SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, E, F
BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C, D, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.69	0.96	26	empty
2	476	0.69	0.80	54	empty
3	56	0.67	0.96	27	empty
4	246	0.62	0.81	30	empty
5	69	0.59	0.89	22	empty

Interfaces

11 interfaces between chains.

C–E · 739 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 722 Å² buried · 12 hydrogen bonds · protein-protein
B–G · 715 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 576 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 518 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (additive adduct).

Compared structures

6HHS · MamM CTD E289D - Cadmium form · 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 Q6NE57
Elsewhere: RCSB PDB 6HHS · PDBe 6HHS · UniProt Q6NE57

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