Example 14: Human Insulin Receptor Ectodomain IRαβ¶

PDB entry 4zxb is a 3.3-Å resolution structure of the human insulin receptor ectodomain (IRαβ) monomer (chain E) in complex two Fabs (chains A, B, C, and D). The receptor is dimeric, and the asymmetric structure is a monomer, so Pestifer replicates the monomer to make a dimer model according to the BIOMT records in the PDB file. The Fabs are excluded. The structure has several missing loops, which Pestifer builds in. The structure also has several glycans, which Pestifer retains.

# Author: Cameron F. Abrams, <cfa22@drexel.edu>
#
# pestifer input script
# 
# Simple build of solvated dimeric insulin receptor ectodomain
#
# Notes:
#   - Missing protein is built-in
#   - Fab chains are excluded
#   - Declashing is turned off
#   - A five-phase NPT equilibration is used to settle the density
#   - A production tarball is generated: prod_4zxb.tgz
#
title: insulin receptor ectodomain, Fabs removed
tasks:
  - fetch:
      sourceID: 4zxb
  - psfgen:
      source:
        biological_assembly: 1
        exclude:
          - chainID in ['A', 'B', 'C', 'D'] 
      mods:
        crotations: # some fine-tuning to ease ligation
          - phi,E,657,693,120
  - md:
      cpu-override: True
      ensemble: minimize
  - ligate:
      steer:
        nsteps: 12000
        temperature: 500
  - validate:
      tests:
        - connection_test:
            name: check ligation
            selection: chain A E and resid 693 694
            connection_type: interresidue
            connection_count: 2 
  - md:
      cpu-override: True
      ensemble: minimize
  - md:
      cpu-override: True
      ensemble: NVT
      nsteps: 24000
  - solvate:
  - md:
      ensemble: minimize
  - md:
      ensemble: NVT
  - md:
      ensemble: NPT
      nsteps: 200
  - md:
      ensemble: NPT
      nsteps: 400
  - md:
      ensemble: NPT
      nsteps: 800
  - md:
      ensemble: NPT
      nsteps: 1600
  - md:
      ensemble: NPT
      nsteps: 13200
  - mdplot:
      timeseries:
        - density
      basename: solvated
      grid: True
  - terminate:
      basename: my_4zxb
      artifacts: artifacts
      package:
        basename: prod_4zxb
        namd:
          ensemble: NPT

Pipeline task summary¶
Step	Task	Details
1	`fetch`	PDB 4ZXB
2	`psfgen`	exclusions, crotations
3	`md`	minimize
4	`ligate`	ligate chain breaks (steered MD, 12,000 steps)
5	`validate`	1 test(s)
6	`md`	minimize → NVT (24,000 steps)
7	`solvate`	water box
8	`md`	minimize → NVT (2,000 steps) → NPT (16,200 steps, 5 phases)
9	`mdplot`	equilibration time-series plots → `mdplots/`
10	`terminate`	basename: `my_4zxb`; package: `prod_4zxb`

../../_images/insulin-receptor-ectodomain.png — Human insulin receptor ectodomain (PDB ID 4zxb) with glycans shown in white licorice. Protein chains are colored uniquely.¶