MolNFT v1 · #52248 · protein

Bjfixlh in ferric form

2VV6 · Sensor protein fixl: “Bjfixlh in ferric form”. X-ray diffraction, 3 ligands (HEM, NA, CL), 6 pockets (best druggability 0.79). MolNFT v1 #52248 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VV6
Type: protein
Length: 423 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sensor protein fixl
EC: 2.7.13.3, 2.7.3.-
UniProt: P23222
Ligands: HEM, NA, CL
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 28% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sensor protein fixl (EC 2.7.13.3, 2.7.3.-)	protein	106	28% helix, 39% strand	P23222
C	Sensor protein fixl (EC 2.7.13.3, 2.7.3.-)	protein	104	29% helix, 39% strand	P23222
D	Sensor protein fixl (EC 2.7.13.3, 2.7.3.-)	protein	107	28% helix, 38% strand	P23222

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 3 copies · chains C, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	260	0.79	0.91	29	HEM
2	759	0.79	0.82	76	HEM
3	276	0.75	0.87	31	HEM
4	264	0.73	0.87	30	HEM
5	148	0.41	0.74	34	empty

Interfaces

5 interfaces between chains.

A–B · 818 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 785 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 394 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 95 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 65 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2VV6 · Bjfixlh in ferric form · the same entry in another collection · chain C against C, TM-score 1.00
P23222 · AlphaFold monomer V2.0 prediction for sensor protein fixl (P23222) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P23222
Elsewhere: RCSB PDB 2VV6 · PDBe 2VV6 · UniProt P23222

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