MolNFT v1 · #169377 · protein

Structure of the tirandamycin C-bound P450 monooxygenase tami

6XA2: “Structure of the tirandamycin C-bound P450 monooxygenase tami”. X-ray diffraction, 2 ligands (HEM, V0A), 20 pockets (best druggability 0.88). MolNFT v1 #169377 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XA2
Type: protein
Length: 3,185 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tami
UniProt: D3Y1J3
Ligands: HEM, V0A
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F, G, H	Tami	protein	399	53% helix, 9% strand	D3Y1J3
C	Tami	protein	393	52% helix, 10% strand	D3Y1J3
D	Tami	protein	398	55% helix, 11% strand	D3Y1J3

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
V0A · (3E)-3-{(2E,4E,6R)-1-hydroxy-4-methyl-6-[(1R,3R,4S,5R)-1,4,8-trimethyl-2,9-dioxabicyclo[3.3.1]non-7-en-3-yl]hepta-2,4-dien-1-ylidene}-2H-pyrrole-2,4(3H)-dione · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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	589	0.88	0.93	71	HEM, V0A
2	594	0.87	0.92	73	HEM, V0A
3	601	0.87	0.92	73	HEM, V0A
4	538	0.87	0.93	68	HEM, V0A
5	555	0.87	0.92	67	HEM, V0A

Interfaces

8 interfaces between chains.

E–G · 1554 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1536 Å² buried · 18 hydrogen bonds · protein-protein
F–H · 1528 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1499 Å² buried · 22 hydrogen bonds · protein-protein
A–E · 397 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6XA2 · Structure of the tirandamycin C-bound P450 monooxygenase TamI · the same entry in another collection · chain A against A, 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 D3Y1J3
Elsewhere: RCSB PDB 6XA2 · PDBe 6XA2 · UniProt D3Y1J3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.