MolNFT v1 · #87051 · protein

Oligopeptidase B from trypanosoma brucei with covalently bound antipain - closed form

4BP9 · Oligopeptidasse B: “Oligopeptidase B from trypanosoma brucei with covalently bound antipain - closed form”. X-ray diffraction, 2 ligands (FC0, OAR), 20 pockets (best druggability 0.77). MolNFT v1 #87051 on GenesisL1: 3D structure…

PDB: 4BP9
Type: protein
Length: 4,272 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligopeptidasse B; Antipain
EC: 3.4.21.83
UniProt: O76728
Ligands: FC0, OAR
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Oligopeptidasse B (EC 3.4.21.83)	protein	710	23% helix, 31% strand	O76728
G, H, I, J, K, L	Antipain	protein	2	0% helix, 0% strand	—

Ligands and binding sites

FC0 · N-carboxy-L-phenylalanine · ligand · 6 copies · chains A, G, B, H, C, I, D, J, E, K, F, L
OAR · N-(4-amino-5-hydroxy-pentyl)-guanidine · ligand · 6 copies · chains A, G, B, H, C, I, D, J, E, K, F, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	961	0.77	0.80	114	empty
2	988	0.77	0.79	82	empty
3	594	0.75	0.82	83	empty
4	802	0.75	0.80	86	empty
5	152	0.75	0.93	25	empty

Interfaces

13 interfaces between chains.

E–F · 1148 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1143 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1138 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 336 Å² buried · 4 hydrogen bonds · protein-protein
F–L · 291 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 covalent (covalent ligand).

Compared structures

4BP9 · Oligopeptidase B from Trypanosoma brucei with covalently bound antipain - closed form · the same entry in another collection · chain B against B, 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 O76728
Elsewhere: RCSB PDB 4BP9 · PDBe 4BP9 · UniProt O76728

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