MolNFT v1 · #184087 · protein

Enterococcus faecalis efrcd in complex with a nanobody

7OCY · ABC transporter ATP-binding protein: “Enterococcus faecalis efrcd in complex with a nanobody”. Electron microscopy, 17 pockets (best druggability 0.85). MolNFT v1 #184087 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7OCY
Type: protein
Length: 1,243 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ABC transporter ATP-binding protein; Nanobody
UniProt: A0A1B4XLV2, A0A1B4XLV0
Pockets: 17 · best druggability 0.85

Structure

electron microscopy · 3 distinct chains · 61% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ABC transporter ATP-binding protein	protein	557	65% helix, 10% strand	A0A1B4XLV2
B	ABC transporter ATP-binding protein	protein	578	68% helix, 8% strand	A0A1B4XLV0
C	Nanobody	protein	108	6% helix, 50% strand	—

Pockets

17 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	775	0.85	0.87	88	empty
2	1194	0.83	0.85	146	empty
3	1131	0.82	0.83	114	empty
4	824	0.79	0.83	116	empty
5	670	0.74	0.80	73	empty

Interfaces

3 interfaces between chains.

A–B · 5199 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 179 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 105 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7OCY · Enterococcus faecalis EfrCD in complex with a nanobody · 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 A0A1B4XLV2
Every structure of UniProt A0A1B4XLV0
Elsewhere: RCSB PDB 7OCY · PDBe 7OCY · UniProt A0A1B4XLV2 · UniProt A0A1B4XLV0

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