PDBScan Report for: /share/apps/genapp/sassie2/results/users/dww100/no_project_specified/1008.pdb

Structure Preparedness for Simulation

Chain Moltype Missing Residues Non-CHARMM Residues Missing Heavy Atoms
A Protein 3 1 0

Oh No! There are critical issues with this PDB!

This PDB is NOT ready for simulation.

  1. Some protein hydrogens are missing - please consult NO_HEADER_PDBSCAN report

  2. Non CHARMM standard residues detected

  3. Missing residues - see table above and full report for details

Warnings

  1. BIOMT present - PDB may not represent the biological unit, see report below

  2. Chains missing segment names will have these created from the chain ID

Summary

CRYSTAL STRUCTURE OF PROJECT ID PH1539 FROM PYROCOCCUS HORIKOSHII OT3

Header HYDROLASE
Citation K.SHIMIZU,C.KUROISHI,M.SUGAHARA,N.KUNISHIMA "STRUCTURE OF PEPTIDYL-TRNA HYDROLASE 2 FROM PYROCOCCUS HORIKOSHII OT3: INSIGHT INTO THE FUNCTIONAL ROLE OF ITS DIMERIC STATE." ACTA CRYSTALLOGR.,SECT.D V. 64 444 2008 Link
Method X-Ray Diffraction
Experiment Resolution 1.20 Angstrom; R-factor 19.30; Free R-factor 21.50; Space Group P 41 21 2

Polymers

Chain ID Name Type No. Sequence Residues % Residues Observed
A PEPTIDYL-TRNA HYDROLASE Protein 121 98

Heterogens

Heterogens may not be included as standard in forcefields.

Residue Name Chain IDs
NA SODIUM ION A

System statistics

Metrics derived from PDB coordinates:

Measurement Value
Number of models 1
Mass 15324.48
Centre of mass 17.85 16.43 33.52
Radius of gyration 14.96
Coordinate minimums 0.88 -6.20 14.78
Coordinate maximums 38.28 40.67 49.46

Biological Unit

Biomolecule: 1 - Author asserted biological unit for chain A: Dimeric

# Rotation Translation
1 1.000000 0.000000 0.000000 0.00000
1 0.000000 1.000000 0.000000 0.00000
1 0.000000 0.000000 1.000000 0.00000
2 0.000000 1.000000 0.000000 0.00000
2 1.000000 0.000000 0.000000 0.00000
2 0.000000 0.000000 -1.000000 85.79100

Chain Information

Sequences provided in FASTA format

Chain A

Sequence:

123456789|123456789|123456789|123456789|123456789|
1 mikMFKYKQVIVARADLKLSKGKLAAQVAHGAVTAAFEAYKKKREWFEAW
51 FREGQKKVVVKVESEEELFKLKAEAEKLGLPNALIRDAGLTEIPPGTVTV
101 LAVGPAPEEIVDKVTGNLKLL-----------------------------
151 --------------------------------------------------
201 --------------------------------------------------
251 --------------------------------------------------
301 --------------------------------------------------
351 --------------------------------------------------
401 --------------------------------------------------
451 --------------------------------------------------
501 --------------------------------------------------
551 --------------------------------------------------
601 --------------------------------------------------
651 --------------------------------------------------
701 --------------------------------------------------
751 --------------------------------------------------
801 --------------------------------------------------
851 --------------------------------------------------
901 --------------------------------------------------
951 --------------------------------------------------
1001 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
1051 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
1101 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
1151 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Gaps:

1-3

Heterogens:

Residue No. Resdiue ID Description
1001 NA SODIUM ION
1002-1188 HOH Water

Chain statistics

Metrics derived from PDB coordinates:

Measurement Value
Number of models 1
Mass 15324.48
Centre of mass 17.85 16.43 33.52
Radius of gyration 14.96
Coordinate minimums 0.88 -6.20 14.78
Coordinate maximums 38.28 40.67 49.46