MolNFT v1 · #137531 · protein

Cryoem structure of the zinc transporter yiip from helical crystals

5VRF · Cadmium and zinc efflux pump fief: “Cryoem structure of the zinc transporter yiip from helical crystals”. Electron microscopy, 1 ligand (ZN), 10 pockets (best druggability 0.79). MolNFT v1 #137531 on GenesisL1: 3D structure, binding…

PDB: 5VRF
Type: protein
Length: 564 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cadmium and zinc efflux pump fief
UniProt: Q8E919
Ligands: ZN
Pockets: 10 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 68% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Cadmium and zinc efflux pump fief	protein	282	68% helix, 10% strand	Q8E919

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains B, A

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

Pockets

10 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	340	0.79	0.89	64	empty
2	677	0.75	0.80	68	empty
3	640	0.74	0.81	68	empty
4	137	0.74	0.93	23	empty
5	59	0.65	0.93	15	empty

Interfaces

1 interface between chains.

B–A · 2592 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5VRF · CryoEM Structure of the Zinc Transporter YiiP from helical crystals · the same entry in another collection · chain B against B, 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 Q8E919
Elsewhere: RCSB PDB 5VRF · PDBe 5VRF · UniProt Q8E919

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