MolNFT v1 · #146177 · protein

Crystal structure of deinococcus radiodurans mnth, an nramp-family transition metal transporter, in the inward-open apo state

6D9W · Divalent metal cation transporter mnth: “Crystal structure of deinococcus radiodurans mnth, an nramp-family transition metal transporter, in the…”. X-ray diffraction, 1 ligand (OS), 14 pockets (best druggability 0.76). MolNFT v1…

PDB: 6D9W
Type: protein
Length: 786 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: 14 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Divalent metal cation transporter mnth	protein	362	80% helix, 0% strand	Q9RTP8
H	Fab heavy chain	protein	211	6% helix, 53% strand	—
L	Fab light chain	protein	213	6% helix, 47% 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

14 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	297	0.76	0.87	60	empty
2	85	0.67	0.92	21	empty
3	253	0.63	0.82	33	empty
4	124	0.53	0.82	24	empty
5	229	0.53	0.77	35	empty

Interfaces

3 interfaces between chains.

H–L · 1785 Å² buried · 13 hydrogen bonds · protein-protein
A–L · 388 Å² buried · 2 hydrogen bonds · protein-protein
A–H · 366 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6D9W · 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 0.87

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 6D9W · PDBe 6D9W · UniProt Q9RTP8

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