Research workbench

Heme D1 biosynthesis associated protein nirf

Analyse Heme D1 biosynthesis associated protein nirf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TV2
Type: protein
Length: 2,976 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein nirf
UniProt: Q51480
Ligands: SO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Protein nirf	protein	372	5% helix, 50% strand	Q51480

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains C, D, G, F, H
GOL · Glycerol · additive · 2 copies · chains B, E, H
MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains E, F

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	904	0.84	0.86	80	empty
2	722	0.83	0.87	77	empty
3	1153	0.83	0.84	92	empty
4	459	0.82	0.89	70	empty
5	715	0.81	0.85	80	empty

Interfaces

12 interfaces between chains.

B–E · 2111 Å² buried · 53 hydrogen bonds · protein-protein
C–G · 2050 Å² buried · 54 hydrogen bonds · protein-protein
C–D · 776 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 582 Å² buried · 10 hydrogen bonds · protein-protein
A–H · 558 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6TV2 · Heme d1 biosynthesis associated Protein NirF · the same entry in another collection · chain H against H, TM-score 1.00
Q51480 · AlphaFold monomer V2.0 prediction for protein nirf (Q51480) · a predicted model of the same protein · chain A 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 Q51480
Elsewhere: RCSB PDB 6TV2 · PDBe 6TV2 · UniProt Q51480

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