MolNFT v1 · #46104 · protein

The structure of the type III effector avrb complexed with a high-affinity RIN4 peptide

2NUD · Avirulence B protein: “The structure of the type III effector avrb complexed with a high-affinity RIN4 peptide”. X-ray diffraction, 5 pockets (best druggability 0.71). MolNFT v1 #46104 on GenesisL1: 3D structure, binding sites and…

PDB: 2NUD
Type: protein
Length: 628 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avirulence B protein; RPM1-interacting protein 4
UniProt: P13835, Q8GYN5
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Avirulence B protein	protein	291	51% helix, 15% strand	P13835
C, D	RPM1-interacting protein 4	protein	23	13% helix, 17% strand	Q8GYN5

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B
ETF · Trifluoroethanol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	386	0.71	0.82	36	TRS, ETF
2	405	0.69	0.81	35	TRS, ETF
3	94	0.35	0.74	22	empty
4	102	0.34	0.73	20	empty
5	71	0.29	0.73	16	empty

Interfaces

3 interfaces between chains.

B–D · 1427 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1419 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 134 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2NUD · The structure of the type III effector AvrB complexed with a high-affinity RIN4 peptide · the same entry in another collection · chain A against A, TM-score 1.00
P13835 · AlphaFold monomer V2.0 prediction for avirulence protein B (P13835) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q8GYN5 · AlphaFold monomer V2.0 prediction for RPM1-interacting protein 4 (Q8GYN5) · a predicted model of the same protein · chain C against A, TM-score 0.18

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 P13835
Every structure of UniProt Q8GYN5
Elsewhere: RCSB PDB 2NUD · PDBe 2NUD · UniProt P13835 · UniProt Q8GYN5

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