SMTL ID : 4ui2.1

Crystal structure of the ternary RGMB-BMP2-NEO1 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 2 residues within 4Å: Chain A: Y.42, N.61 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain E: Y.42, N.61 No protein-ligand interaction detected (PLIP)

6 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.2: 4 residues within 4Å: Chain B: R.16, H.17, P.18, F.41 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.16 Salt bridges: B:R.16 SRT.3: 2 residues within 4Å: Chain B: Y.20, H.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.39 Salt bridges: B:H.39 SRT.4: 8 residues within 4Å: Chain B: K.101, N.102, Y.103, Q.104 Chain C: G.55, N.56, L.57 Chain F: N.59 7 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F, 4 interactions with chain B Hydrogen bonds: C:L.57, F:N.59, F:N.59, B:K.101, B:Q.104 Salt bridges: B:K.101, B:K.101 SRT.7: 4 residues within 4Å: Chain F: R.16, H.17, P.18, F.41 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.16 Salt bridges: F:R.16 SRT.8: 2 residues within 4Å: Chain F: Y.20, H.39 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.39 Salt bridges: F:H.39 SRT.9: 8 residues within 4Å: Chain B: N.59 Chain F: K.101, N.102, Y.103, Q.104 Chain G: G.55, N.56, L.57 7 PLIP interactions: 2 interactions with chain B, 4 interactions with chain F, 1 interactions with chain G Hydrogen bonds: B:N.59, B:N.59, F:K.101, F:Q.104, G:L.57 Salt bridges: F:K.101, F:K.101

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 2 residues within 4Å: Chain B: P.35, S.88 No protein-ligand interaction detected (PLIP) ACT.10: 2 residues within 4Å: Chain F: P.35, S.88 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Healey, E.G. et al., Repulsive Guidance Molecule is a Structural Bridge between Neogenin and Bone Morphogenetic Protein. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-05-06

Peptides

NEOGENIN: AE
BONE MORPHOGENETIC PROTEIN 2, BMP2: BF
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN: CG
REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

B
B

F
B

C
C

G
C

D
D

H
D

NEOGENIN

BONE MORPHOGENETIC PROTEIN 2, BMP2

REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN

REPULSIVE GUIDANCE MOLECULE C, RGMC, HEMOJUVELIN

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