MolNFT v1 · #52036 · protein

Fe-FUTA2 from synechocystis PCC6803

2VP1 · Periplasmic iron-binding protein: “Fe-FUTA2 from synechocystis PCC6803”. X-ray diffraction, 2 ligands (FE, CL), 5 pockets (best druggability 0.60). MolNFT v1 #52036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VP1
Type: protein
Length: 626 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Periplasmic iron-binding protein
UniProt: Q55835
Ligands: FE, CL
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Periplasmic iron-binding protein	protein	313	45% helix, 18% strand	Q55835

Ligands and binding sites

FE · Fe (III) ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B

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

Pockets

5 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	300	0.60	0.79	42	empty
2	460	0.60	0.75	63	empty
3	103	0.38	0.75	21	CL
4	68	0.31	0.75	18	empty
5	59	0.29	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 604 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2VP1 · Fe-FutA2 from Synechocystis PCC6803 · the same entry in another collection · chain A against A, TM-score 1.00
Q55835 · AlphaFold monomer V2.0 prediction for iron uptake protein A2 (Q55835) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q55835
Elsewhere: RCSB PDB 2VP1 · PDBe 2VP1 · UniProt Q55835

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