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Crystal structure of deinococcus radiodurans mnth, an nramp-family transition metal transporter

Analyse Crystal structure of deinococcus radiodurans mnth, an nramp-family transition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KTE
Type: protein
Length: 762 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Divalent metal cation transporter mnth; Fab heavy chain; Fab light chain
UniProt: Q9RTP8
Ligands: OS
Pockets: 12 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Divalent metal cation transporter mnth	protein	338	72% helix, 0% strand	Q9RTP8
H	Fab heavy chain	protein	211	3% helix, 48% strand	—
L	Fab light chain	protein	213	5% helix, 48% strand	—

Ligands and binding sites

OS · Osmium ion · metal · 3 copies · chains H

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

Pockets

12 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	538	0.70	0.79	56	empty
2	87	0.67	0.91	24	empty
3	228	0.65	0.84	44	empty
4	443	0.63	0.76	44	empty
5	300	0.53	0.75	40	empty

Interfaces

3 interfaces between chains.

H–L · 1788 Å² buried · 13 hydrogen bonds · protein-protein
A–H · 359 Å² buried · 6 hydrogen bonds · protein-protein
A–L · 353 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5KTE · Crystal structure of Deinococcus radiodurans MntH, an Nramp-family transition metal… · the same entry in another collection · chain A against A, TM-score 1.00
Q9RTP8 · AlphaFold monomer V2.0 prediction for divalent metal cation transporter mnth (Q9RTP8) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 Q9RTP8
Elsewhere: RCSB PDB 5KTE · PDBe 5KTE · UniProt Q9RTP8

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