SMTL ID : 2ifg.1

Structure of the extracellular segment of human TRKA in complex with nerve growth factor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NDG.1: 2 residues within 4Å: Chain A: R.122, N.153 No protein-ligand interaction detected (PLIP) NAG-NDG.7: 4 residues within 4Å: Chain B: R.122, E.129, N.153, A.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.122, B:R.122, B:E.129, B:E.129

4 x NAG- NDG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NDG-MAN.2: 3 residues within 4Å: Chain A: N.227, S.242, Q.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.227, A:S.242, A:S.242, A:Q.244, A:N.303 NAG-NDG-MAN.5: 5 residues within 4Å: Chain A: E.35, R.59, N.60, R.84 Ligands: NAG-NDG-BMA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.59, A:R.84 NAG-NDG-MAN.8: 2 residues within 4Å: Chain B: N.227, S.242 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.227, B:S.242, B:S.242 NAG-NDG-MAN.11: 6 residues within 4Å: Chain B: E.35, Y.37, R.59, N.60, R.84 Ligands: NAG-NDG-BMA.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.35, B:R.59, B:R.84, B:R.84

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

NAG-NDG-BMA.3: 3 residues within 4Å: Chain A: R.225, N.246, Q.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.225, A:N.246, A:Q.273 NAG-NDG-BMA.4: 2 residues within 4Å: Chain A: N.323, M.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.323 NAG-NDG-BMA.6: 5 residues within 4Å: Chain A: T.62, N.86, S.88, F.89 Ligands: NAG-NDG-MAN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88 NAG-NDG-BMA.9: 3 residues within 4Å: Chain B: R.225, N.246, Q.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.225, B:Q.273 NAG-NDG-BMA.10: 3 residues within 4Å: Chain B: N.323, S.338, M.340 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.323 NAG-NDG-BMA.12: 6 residues within 4Å: Chain B: V.64, N.86, S.88, F.89, V.109 Ligands: NAG-NDG-MAN.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.88 Hydrophobic interactions: B:F.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wehrman, T. et al., Structural and mechanistic insights into nerve growth factor interactions with the TrkA and p75 receptors. Neuron (2007)

Release Date

2007-02-13

Peptides

High affinity nerve growth factor receptor: AB
Beta-nerve growth factor: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

High affinity nerve growth factor receptor

Beta-nerve growth factor

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