MolNFT v1 · #58628 · protein

Crystal structure of human grp crd

3B9C · HSPC159: “Crystal structure of human grp crd”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.40). MolNFT v1 #58628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3B9C
Type: protein
Length: 536 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HSPC159
UniProt: Q9P005
Ligands: SO4
Pockets: 8 · best druggability 0.40

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, C, B	HSPC159	protein	134	2% helix, 59% strand	Q9P005

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, B, D, C
BME · Beta-mercaptoethanol · additive · 6 copies · chains A, D, C, B

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

Pockets

8 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	118	0.40	0.75	20	empty
2	176	0.39	0.71	23	SO4
3	98	0.37	0.75	22	empty
4	97	0.36	0.74	16	empty
5	84	0.33	0.74	20	empty

Interfaces

6 interfaces between chains.

A–B · 382 Å² buried · 13 hydrogen bonds · protein-protein
D–C · 380 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 120 Å² buried · 1 hydrogen bond · protein-protein
C–B · 97 Å² buried · 1 hydrogen bond · protein-protein
A–C · 75 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3B9C · Crystal Structure of Human GRP CRD · 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 Q9P005
Elsewhere: RCSB PDB 3B9C · PDBe 3B9C · UniProt Q9P005

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