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Human myeloid-derived growth factor (mydgf) in complex with neutralizing Fab

Analyse Human myeloid-derived growth factor (mydgf) in complex with neutralizing Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SVL
Type: protein
Length: 3,231 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: FAB_HEAVY_CHAIN; FAB_LIGHT_CHAIN; Myeloid-derived growth factor
UniProt: Q969H8
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 12 distinct chains · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	FAB_HEAVY_CHAIN	protein	212	8% helix, 50% strand	—
B	FAB_LIGHT_CHAIN	protein	210	6% helix, 50% strand	—
C	Myeloid-derived growth factor	protein	95	3% helix, 51% strand	Q969H8
D, H, K, O	FAB_HEAVY_CHAIN	protein	213	8% helix, 50% strand	—
E, I, L, M	FAB_LIGHT_CHAIN	protein	212	6% helix, 51% strand	—
F	Myeloid-derived growth factor	protein	116	3% helix, 58% strand	Q969H8
G	FAB_HEAVY_CHAIN	protein	215	8% helix, 51% strand	—
J	Myeloid-derived growth factor	protein	126	2% helix, 57% strand	Q969H8
N	Myeloid-derived growth factor	protein	123	5% helix, 59% strand	Q969H8
P	FAB_LIGHT_CHAIN	protein	191	4% helix, 49% strand	—
Q	Myeloid-derived growth factor	protein	123	2% helix, 59% strand	Q969H8
R	Myeloid-derived growth factor	protein	120	5% helix, 57% strand	Q969H8

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains D, E, M, O, P, R

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	985	0.82	0.83	76	empty
2	860	0.72	0.77	90	empty
3	821	0.70	0.76	70	empty
4	559	0.67	0.77	66	empty
5	484	0.67	0.79	90	GOL

Interfaces

40 interfaces between chains.

O–P · 1871 Å² buried · 12 hydrogen bonds · protein-protein
G–I · 1869 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 1862 Å² buried · 16 hydrogen bonds · protein-protein
H–L · 1857 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1846 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 disulfide (disulfide).

Compared structures

6SVL · human Myeloid-derived growth factor (MYDGF) in complex with neutralizing Fab · the same entry in another collection · chain R against R, 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 Q969H8
Elsewhere: RCSB PDB 6SVL · PDBe 6SVL · UniProt Q969H8

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