MolNFT v1 · #151376 · protein

Structure in P1 form of the pbp agtb in complex with agropinic acid from A.TUMEFACIEN R10

6HM2 · Agropine permease: “Structure in P1 form of the pbp agtb in complex with agropinic acid from A.TUMEFACIEN R10”. X-ray diffraction, 2 ligands (G9Z, NA), 15 pockets (best druggability 0.79). MolNFT v1 #151376 on GenesisL1: 3D…

PDB: 6HM2
Type: protein
Length: 1,573 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agropine permease
UniProt: W8FRA6
Ligands: G9Z, NA
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Agropine permease	protein	316	46% helix, 20% strand	W8FRA6
B	Agropine permease	protein	317	45% helix, 20% strand	W8FRA6
C, D	Agropine permease	protein	314	46% helix, 20% strand	W8FRA6
E	Agropine permease	protein	312	46% helix, 20% strand	W8FRA6

Ligands and binding sites

G9Z · agropinic acid · ligand · 5 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, B, C

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

Pockets

15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.79	0.81	80	G9Z
2	409	0.74	0.84	46	empty
3	1098	0.74	0.77	71	EDO
4	684	0.73	0.80	67	empty
5	288	0.71	0.85	40	G9Z, NA

Interfaces

7 interfaces between chains.

B–D · 571 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 544 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 411 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 393 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 214 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6HM2 · Structure in P1 form of the PBP AgtB in complex with agropinic acid from A.tumefacien R10 · the same entry in another collection · chain C against C, 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 W8FRA6
Elsewhere: RCSB PDB 6HM2 · PDBe 6HM2 · UniProt W8FRA6

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