MolNFT v1 · #115219 · protein

Structure of immature VRC01-class antibody DRVIA7

5CD3 · DRVIA7 heavy chain: “Structure of immature VRC01-class antibody DRVIA7”. X-ray diffraction, 17 pockets (best druggability 0.84). MolNFT v1 #115219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CD3
Type: protein
Length: 1,704 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DRVIA7 heavy chain; DRVIA7 light chain
Pockets: 17 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, A, C, E	DRVIA7 heavy chain	protein	220	7% helix, 50% strand	—
H, B, D, F	DRVIA7 light chain	protein	206	7% helix, 50% strand	—

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1118	0.84	0.85	118	empty
2	652	0.74	0.81	43	empty
3	823	0.74	0.79	98	empty
4	593	0.73	0.81	43	empty
5	244	0.70	0.86	53	empty

Interfaces

14 interfaces between chains.

G–H · 1826 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1812 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1803 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1792 Å² buried · 18 hydrogen bonds · protein-protein
G–D · 794 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5CD3 · Structure of immature VRC01-class antibody DRVIA7 · the same entry in another collection · chain G against G, 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
Elsewhere: RCSB PDB 5CD3 · PDBe 5CD3

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