PDBIHM.org

PDB-IHM

System for Archiving Integrative Structures

Ensemble information?

This entry consists of 0 distinct ensemble.

Summary?

This entry consists of 1 model(s). A total of 3 datasets were used to build this entry.

Representation ?

This entry has 1 representation(s).

ID Model(s) Entity ID Molecule name Chain(s) [auth] Total residues Rigid segments Flexible segments Model coverage/
Starting model coverage
(%)		 Scale
1 1 1 Protein-glutamine gamma-glutamyltransferase 2 A 687 - 1-687 100.00 /
100.00 		Atomic
2 Fibronectin B 90 - 1-90 100.00 /
100.00 		Atomic

Datasets used for modeling ?

There are 3 unique datasets used to build the models in this entry.
ID Dataset type Database name Data access code
1
Crosslinking-MS data
PRIDE
2
Experimental model
PDB
3
Experimental model
PDB

Methodology and software?

This entry is a result of 1 distinct protocol.
Step number Protocol ID Method name Method type Method description Number of computed models Multi state modeling Multi scale modeling
1
1
Refinement
Iterative Threading ASSEmbly Refinement
structural refinement of starting models guided by experimental crosslinks
None
False
False
2
1
satisfied/violated crosslinks identification
Validate measured chemical cross-links on a protein 3D structure
calculation of Euclidean distances between crosslinked residues
None
False
False
3
1
calculation of accessible area
calculates the atomic accessible area when a probe is rolled around the Van der Waal's surface of a macromolecule
calculation of accessible area
None
False
False
4
1
accessible interaction space
None
determine the number of complexes consistent with the restraints
None
False
False
5
1
docking
data-driven biomolecular docking
generates predicted model of a protein complex
None
False
False
There are 5 software packages reported in this entry.
ID Software name Software version Software classification Software location
1
Not available
structure refinement
3
Not available
Euclidean distances calculation
2
Not available
solvent accessibility
4
Not available
accessible interaction space
5
Not available
protein-protein docking