MolNFT v1 · #171403 · protein

Repulsive guidance molecule B (rgmb) in complex with growth differentiation factor 5 (GDF5) and neogenin 1 (NEO1)

6Z3M · GROWTH/DIFFERENTIATION factor 5: “Repulsive guidance molecule B (rgmb) in complex with growth differentiation factor 5 (GDF5) and neogenin 1…”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.68). MolNFT v1…

PDB: 6Z3M
Type: protein
Length: 3,257 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GROWTH/DIFFERENTIATION factor 5; Rgm domain family member B; Neogenin
UniProt: P43026, Q6NW40, P97798
Ligands: NAG
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 12 distinct chains · 28% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H, M	GROWTH/DIFFERENTIATION factor 5	protein	105	17% helix, 45% strand	P43026
B, G, N	GROWTH/DIFFERENTIATION factor 5	protein	106	17% helix, 44% strand	P43026
C	Rgm domain family member B	protein	74	68% helix, 0% strand	Q6NW40
D	Rgm domain family member B	protein	75	60% helix, 0% strand	Q6NW40
E, F, K, Q, R	Neogenin	protein	205	1% helix, 49% strand	P97798
I	Rgm domain family member B	protein	71	63% helix, 0% strand	Q6NW40
J	Rgm domain family member B	protein	73	68% helix, 0% strand	Q6NW40
L	Neogenin	protein	187	0% helix, 50% strand	P97798
O	Rgm domain family member B	protein	71	70% helix, 0% strand	Q6NW40
P	Rgm domain family member B	protein	76	59% helix, 0% strand	Q6NW40
c, d, i, j, o, p	Rgm domain family member B	protein	158	9% helix, 47% strand	Q6NW40
S, T, U, V, W, X	Rgm domain family member B	protein	4	0% helix, 0% strand	Q6NW40

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains D, E, F, I, K, L, P, Q, 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	515	0.68	0.78	74	empty
2	492	0.68	0.79	61	empty
3	191	0.66	0.85	33	empty
4	423	0.66	0.79	59	empty
5	194	0.64	0.84	33	empty

Interfaces

34 interfaces between chains.

R–p · 1233 Å² buried · 18 hydrogen bonds · protein-protein
F–d · 1232 Å² buried · 18 hydrogen bonds · protein-protein
L–j · 1232 Å² buried · 18 hydrogen bonds · protein-protein
Q–o · 1231 Å² buried · 18 hydrogen bonds · protein-protein
E–c · 1231 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 57 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

6Z3M · Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5… · the same entry in another collection · chain K against K, 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 P43026
Every structure of UniProt Q6NW40
Every structure of UniProt P97798
Elsewhere: RCSB PDB 6Z3M · PDBe 6Z3M · UniProt P43026 · UniProt Q6NW40 · UniProt P97798

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