MolNFT v1 · #113854 · protein

Crystal structure of the hypab-ni complex

5AUN · Probable hydrogenase nickel incorporation protein hypa: “Crystal structure of the hypab-ni complex”. X-ray diffraction, 6 ligands (URE, ADP, MG), 2 pockets (best druggability 0.40). MolNFT v1 #113854 on GenesisL1: 3D structure…

PDB: 5AUN
Type: protein
Length: 376 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable hydrogenase nickel incorporation protein hypa; ATPase involved in chromosome…
UniProt: Q5JIH3, Q5JIH4
Ligands: URE, ADP, MG, ZN, NI, CL
Pockets: 2 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable hydrogenase nickel incorporation protein hypa	protein	136	40% helix, 28% strand	Q5JIH3
B	ATPase involved in chromosome partitioning, PARA/MIND family, mrp homolog	protein	240	39% helix, 22% strand	Q5JIH4

Ligands and binding sites

URE · Urea · ligand · 3 copies · chains A
ADP · Adenosine-5'-diphosphate · ligand · chains B
MG · Magnesium ion · metal · 2 copies · chains B
ZN · Zinc ion · metal · chains A
NI · Nickel (II) ion · metal · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	125	0.40	0.75	24	ADP, MG
2	68	0.30	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 273 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5AUN · Crystal structure of the HypAB-Ni complex · the same entry in another collection · chain A against A, TM-score 1.00
Q5JIH3 · AlphaFold monomer V2.0 prediction for hydrogenase maturation factor hypa (Q5JIH3) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q5JIH3
Every structure of UniProt Q5JIH4
Elsewhere: RCSB PDB 5AUN · PDBe 5AUN · UniProt Q5JIH3 · UniProt Q5JIH4

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