5LSP

107_A07 Fab in complex with fragment of the Met receptor

PDB DOI: https://doi.org/10.2210/pdb5LSP/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Homo sapiens
Mutation(s): No

Deposited: 2016-09-05 Released: 2017-09-13
Deposition Author(s): DiCara, D., Chirgadze, D.Y., Pope, A., Karatt-Vellatt, A., Winter, A., van den Heuvel, J., Gherardi, E., McCafferty, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.257
R-Value Work: 0.215
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 149.68 kDa
Atom Count: 10,159
Modelled Residue Count: 1,319
Deposited Residue Count: 1,368
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A, D [auth P]	231	Homo sapiens	Mutation(s): 0 Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581 Go to UniProtKB: P08581
PHAROS: P08581 GTEx: ENSG00000105976
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08581
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
107_A07 Fab heavy chain	B [auth H], E [auth S]	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
107_A07 Fab light chain	C [auth L], F [auth T]	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	G [auth X], H [auth Y]	14	Homo sapiens	Mutation(s): 0 Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581 Go to UniProtKB: P08581
PHAROS: P08581 GTEx: ENSG00000105976
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08581
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth P] SDF format, chain I [auth A] MOL2 format, chain J [auth P] MOL2 format, chain I [auth A]	I [auth A], J [auth P]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth P] Interactions & Density Focus chain I [auth A] Focus chain J [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.257
R-Value Work: 0.215
R-Value Observed: 0.217
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.88	α = 90
b = 82.279	β = 90
c = 267.304	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-09-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-13
Type: Initial release
Version 1.1: 2018-01-24
Changes: Source and taxonomy
Version 1.2: 2019-02-20
Changes: Advisory, Data collection, Derived calculations
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary