MolNFT v1 · #56746 · protein

The nature of the TRAP:ANTI-trap complex

2ZP9 · Transcription attenuation protein mtrb: “The nature of the TRAP:ANTI-trap complex”. X-ray diffraction, 2 ligands (TRP, ZN), 16 pockets (best druggability 0.78). MolNFT v1 #56746 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 2ZP9
Type: protein
Length: 741 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription attenuation protein mtrb; Tryptophan RNA-binding attenuator…
UniProt: Q9X6J6, O31466
Ligands: TRP, ZN
Pockets: 16 · best druggability 0.78

Structure

x-ray diffraction · 9 distinct chains · 24% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, G, K, L	Transcription attenuation protein mtrb	protein	63	0% helix, 60% strand	Q9X6J6
B	Transcription attenuation protein mtrb	protein	64	0% helix, 58% strand	Q9X6J6
C	Tryptophan RNA-binding attenuator protein-inhibitory protein	protein	46	28% helix, 13% strand	O31466
D	Tryptophan RNA-binding attenuator protein-inhibitory protein	protein	45	36% helix, 9% strand	O31466
E	Tryptophan RNA-binding attenuator protein-inhibitory protein	protein	49	33% helix, 12% strand	O31466
H, M	Tryptophan RNA-binding attenuator protein-inhibitory protein	protein	42	31% helix, 5% strand	O31466
I	Tryptophan RNA-binding attenuator protein-inhibitory protein	protein	39	33% helix, 5% strand	O31466
J, O	Tryptophan RNA-binding attenuator protein-inhibitory protein	protein	41	32% helix, 15% strand	O31466
N	Tryptophan RNA-binding attenuator protein-inhibitory protein	protein	17	76% helix, 0% strand	O31466

Ligands and binding sites

TRP · Tryptophan · ligand · 6 copies · chains A, B, F, G, K, L
ZN · Zinc ion · metal · 5 copies · chains C, D, E, I, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.78	0.98	20	TRP
2	96	0.77	0.98	20	TRP
3	93	0.76	0.97	21	TRP
4	93	0.75	0.97	19	TRP
5	199	0.50	0.77	29	empty

Interfaces

31 interfaces between chains.

A–B · 920 Å² buried · 13 hydrogen bonds · protein-protein
F–G · 913 Å² buried · 13 hydrogen bonds · protein-protein
G–K · 908 Å² buried · 19 hydrogen bonds · protein-protein
K–L · 898 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 695 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2ZP9 · The Nature of the TRAP:Anti-TRAP complex · the same entry in another collection · chain K against K, 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 Q9X6J6
Every structure of UniProt O31466
Elsewhere: RCSB PDB 2ZP9 · PDBe 2ZP9 · UniProt Q9X6J6 · UniProt O31466

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