MolNFT v1 · #140710 · protein

Crystal structure of HIRA(644-1017)

5YJE · Protein hira: “Crystal structure of HIRA(644-1017)”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.75). MolNFT v1 #140710 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YJE
Type: protein
Length: 932 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein hira
UniProt: P54198
Ligands: SO4
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein hira	protein	315	30% helix, 36% strand	P54198
B	Protein hira	protein	318	28% helix, 34% strand	P54198
C	Protein hira	protein	299	28% helix, 38% strand	P54198

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B, C

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	207	0.75	0.90	43	empty
2	223	0.73	0.88	39	empty
3	348	0.72	0.84	52	empty
4	359	0.69	0.82	41	empty
5	367	0.68	0.81	38	empty

Interfaces

3 interfaces between chains.

A–B · 1554 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1535 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1501 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5YJE · Crystal structure of HIRA(644-1017) · the same entry in another collection · chain A against A, TM-score 1.00
P54198 · AlphaFold monomer V2.0 prediction for protein hira (P54198) · 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 P54198
Elsewhere: RCSB PDB 5YJE · PDBe 5YJE · UniProt P54198

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