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Human angiogenin pd variant Q77P

Analyse Human angiogenin pd variant Q77P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M9M
Type: protein
Length: 476 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Angiogenin
EC: 3.1.27.-
UniProt: P03950
Ligands: SO4
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 26% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Angiogenin (EC 3.1.27.-)	protein	120	27% helix, 37% strand	P03950
B	Angiogenin (EC 3.1.27.-)	protein	121	26% helix, 36% strand	P03950
C	Angiogenin (EC 3.1.27.-)	protein	116	26% helix, 33% strand	P03950
D	Angiogenin (EC 3.1.27.-)	protein	119	26% helix, 37% strand	P03950

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
PGE · Triethylene glycol · additive · 2 copies · chains A, C, D
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	961	0.70	0.75	80	SO4
2	105	0.36	0.74	19	empty

Interfaces

6 interfaces between chains.

A–D · 475 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 377 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 375 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 315 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 69 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

5M9M · Human angiogenin PD variant Q77P · the same entry in another collection · chain D against D, TM-score 1.00
P03950 · AlphaFold monomer V2.0 prediction for angiogenin (P03950) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P03950
Elsewhere: RCSB PDB 5M9M · PDBe 5M9M · UniProt P03950

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