MolNFT v1 · #153252 · protein

Crystal structure of hind apo

6J85 · Nocardicin N-oxygenase: “Crystal structure of hind apo”. X-ray diffraction, 1 ligand (HEM), 10 pockets (best druggability 0.88). MolNFT v1 #153252 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6J85
Type: protein
Length: 790 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nocardicin N-oxygenase
UniProt: A0A1M4Y7D5
Ligands: HEM
Pockets: 10 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nocardicin N-oxygenase	protein	395	53% helix, 10% strand	A0A1M4Y7D5

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	635	0.88	0.92	63	HEM
2	617	0.86	0.90	64	HEM
3	945	0.77	0.80	90	empty
4	168	0.57	0.81	23	empty
5	197	0.53	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 845 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6J85 · Crystal structure of HinD apo · the same entry in another collection · chain A against A, 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 A0A1M4Y7D5
Elsewhere: RCSB PDB 6J85 · PDBe 6J85 · UniProt A0A1M4Y7D5

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