MolNFT v1 · #114189 · protein

Crystal structure of plexin inhibitor complex

5B4W · Plexin-B1: “Crystal structure of plexin inhibitor complex”. X-ray diffraction, 3 ligands (ACE, NAG, NH2), 20 pockets (best druggability 0.83). MolNFT v1 #114189 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B4W
Type: protein
Length: 2,758 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plexin-B1; Synthesized cyclic peptide
UniProt: O43157
Ligands: ACE, NAG, NH2
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Plexin-B1	protein	434	7% helix, 41% strand	O43157
C	Plexin-B1	protein	442	8% helix, 41% strand	O43157
D	Plexin-B1	protein	436	8% helix, 40% strand	O43157
E	Plexin-B1	protein	478	9% helix, 40% strand	O43157
F	Plexin-B1	protein	438	8% helix, 41% strand	O43157
G, H, I, J, K, L	Synthesized cyclic peptide	protein	16	0% helix, 25% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 6 copies · chains B, G, A, H, D, I, C, J, F, K, E, L
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D, E, F
NH2 · Amino group · ion · 6 copies · chains B, G, A, H, D, I, C, J, F, K, E, 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	234	0.83	0.95	39	empty
2	189	0.82	0.96	32	empty
3	1184	0.81	0.83	108	empty
4	192	0.81	0.95	28	empty
5	1009	0.79	0.80	91	empty

Interfaces

18 interfaces between chains.

C–D · 820 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 746 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 735 Å² buried · 13 hydrogen bonds · protein-protein
E–K · 720 Å² buried · 12 hydrogen bonds · protein-protein
A–G · 715 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 33 disulfide, 12 covalent, 7 glycan, 6 d-amino (disulfide, covalent ligand, N-glycosylation, D-amino acid).

Compared structures

O43157 · AlphaFold monomer V2.0 prediction for plexin-B1 (O43157) · a predicted model of the same protein · chain D 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 O43157
Elsewhere: RCSB PDB 5B4W · PDBe 5B4W · UniProt O43157

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