› 6svl

X-ray diffraction
1.58Å resolution

human Myeloid-derived growth factor (MYDGF) in complex with neutralizing Fab

Released:
DOI: 10.2210/pdb6svl/pdb
PDB entry 6svl coloured by chain, front view.
PDB entry 6svl coloured by chain, side view.
PDB entry 6svl coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure and receptor-interacting residues of MYDGF - a protein mediating ischemic tissue repair.
Ebenhoch R, Akhdar A, Reboll MR, Korf-Klingebiel M, Gupta P, Armstrong J, Huang Y, Frego L, Rybina I, Miglietta J, Pekcec A, Wollert KC, Nar H
OpenAccess logo Nat Commun 10 5379 (2019)
PMID: 31772377

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212678 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fab_heavy_chain Chains: A, D, G, H, K, O
Molecule details ›
Chains: A, D, G, H, K, O
Length: 244 amino acids
Theoretical weight: 26.56 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Fab_light_chain Chains: B, E, I, L, M, P
Molecule details ›
Chains: B, E, I, L, M, P
Length: 234 amino acids
Theoretical weight: 25.63 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Myeloid-derived growth factor Chains: C, F, J, N, Q, R
Molecule details ›
Chains: C, F, J, N, Q, R
Length: 142 amino acids
Theoretical weight: 15.85 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q969H8 (Residues: 32-173; Coverage: 100%)
Gene names: C19orf10, MYDGF
Sequence domains: UPF0556 domain

Ligands and Environments

1 bound ligand:
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P1
Unit cell:
a: 89.519Å b: 107.43Å c: 109.369Å
α: 71.54° β: 86.25° γ: 73.38°
R-values:
R R work R free
0.182 0.181 0.206
Expression system: Homo sapiens

Quick links

Citations

2 review citations

Myeloid-derived growth factor in diseases: structure, function and mechanisms.
Chen et al. (2024)
1 more

2 mentions without citation

Scap structures highlight key role for rotation of intertwined luminal loops in cholesterol sensing.
Kober et al. (2021)
1 more