MolNFT v1 · #161984 · protein

Structure of atpgs-bound outward-facing TM287/288 in complex with nanobody NB_TM#2

6QV2 · ABC transporter, ATP-binding protein: “Structure of atpgs-bound outward-facing TM287/288 in complex with nanobody NB_TM#2”. X-ray diffraction, 2 ligands (AGS, MG), 20 pockets (best druggability 0.87). MolNFT v1 #161984 on GenesisL1…

PDB: 6QV2
Type: protein
Length: 2,534 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter, ATP-binding protein; Uncharacterized ABC transporter ATP-binding protein…
UniProt: Q9WYC3, Q9WYC4
Ligands: AGS, MG
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	ABC transporter, ATP-binding protein	protein	568	60% helix, 11% strand	Q9WYC3
B, D	Uncharacterized ABC transporter ATP-binding protein TM_0288	protein	570	61% helix, 9% strand	Q9WYC4
E, F	NB_TM NO.2	protein	129	0% helix, 28% strand	—

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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	954	0.87	0.89	109	empty
2	1102	0.87	0.88	105	AGS, MG
3	1069	0.87	0.88	103	AGS, MG
4	807	0.86	0.88	86	empty
5	1025	0.80	0.81	107	AGS, MG

Interfaces

7 interfaces between chains.

A–B · 7866 Å² buried · 62 hydrogen bonds · protein-protein
C–D · 7655 Å² buried · 60 hydrogen bonds · protein-protein
B–E · 707 Å² buried · 5 hydrogen bonds · protein-protein
D–F · 680 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 99 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6QV2 · Structure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2 · the same entry in another collection · chain C against C, TM-score 1.00
Q9WYC4 · AlphaFold monomer V2.0 prediction for uncharacterized ABC transporter ATP-binding protein… · a predicted model of the same protein · chain B against A, TM-score 0.71

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 Q9WYC3
Every structure of UniProt Q9WYC4
Elsewhere: RCSB PDB 6QV2 · PDBe 6QV2 · UniProt Q9WYC3 · UniProt Q9WYC4

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