5T5O

LECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH TN-PEPTIDE

PDB DOI: https://doi.org/10.2210/pdb5T5O/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bauhinia forficata, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-31 Released: 2016-12-28
Deposition Author(s): Lubkowski, J., Wlodawer, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.230
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 279.05 kDa
Atom Count: 18,803
Modelled Residue Count: 2,350
Deposited Residue Count: 2,480
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A C [auth B] E [auth C] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J]	242	Bauhinia forficata	Mutation(s): 0
UniProt
Find proteins for P86993 (Bauhinia forficata) Explore P86993 Go to UniProtKB: P86993
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P86993
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TN-peptide ACE-GLY-VAL-THR-SER-ALA	B [auth a] D [auth b] F [auth c] H [auth d] J [auth e] B [auth a], D [auth b], F [auth c], H [auth d], J [auth e], L [auth f], N [auth g], P [auth h], R [auth i], T [auth j]	6	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain CA [auth c] SDF format, chain FA [auth d] SDF format, chain IA [auth e] SDF format, chain LA [auth f] SDF format, chain OA [auth g] SDF format, chain RA [auth h] SDF format, chain UA [auth i] SDF format, chain W [auth a] SDF format, chain Z [auth b] SDF format, chain XA [auth j] MOL2 format, chain CA [auth c] MOL2 format, chain FA [auth d] MOL2 format, chain IA [auth e] MOL2 format, chain LA [auth f] MOL2 format, chain OA [auth g] MOL2 format, chain RA [auth h] MOL2 format, chain UA [auth i] MOL2 format, chain W [auth a] MOL2 format, chain Z [auth b] MOL2 format, chain XA [auth j]	CA [auth c] FA [auth d] IA [auth e] LA [auth f] OA [auth g] CA [auth c], FA [auth d], IA [auth e], LA [auth f], OA [auth g], RA [auth h], UA [auth i], W [auth a], XA [auth j], Z [auth b]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain CA [auth c] Focus chain FA [auth d] Focus chain IA [auth e] Focus chain LA [auth f] Focus chain OA [auth g] Focus chain RA [auth h] Focus chain UA [auth i] Focus chain W [auth a] Focus chain XA [auth j] Focus chain Z [auth b] Interactions & Density Focus chain CA [auth c] Focus chain FA [auth d] Focus chain IA [auth e] Focus chain LA [auth f] Focus chain OA [auth g] Focus chain RA [auth h] Focus chain UA [auth i] Focus chain W [auth a] Focus chain XA [auth j] Focus chain Z [auth b]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain DA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain JA [auth F] SDF format, chain KA [auth F] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain PA [auth H] SDF format, chain QA [auth H] SDF format, chain SA [auth I] SDF format, chain TA [auth I] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth J] SDF format, chain WA [auth J] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain EA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain PA [auth H] MOL2 format, chain QA [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth J] MOL2 format, chain WA [auth J] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain EA [auth D]	AA [auth C] BA [auth C] DA [auth D] EA [auth D] GA [auth E] AA [auth C], BA [auth C], DA [auth D], EA [auth D], GA [auth E], HA [auth E], JA [auth F], KA [auth F], MA [auth G], NA [auth G], PA [auth H], QA [auth H], SA [auth I], TA [auth I], U [auth A], V [auth A], VA [auth J], WA [auth J], X [auth B], Y [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth J] Focus chain WA [auth J] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth J] Focus chain WA [auth J] Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.230
R-Value Work: 0.201
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.081	α = 90
b = 187.29	β = 90
c = 258.387	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Lubkowski, J.

Wlodawer, A.

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2017-02-08
Changes: Database references
Version 1.2: 2017-02-15
Changes: Database references
Version 1.3: 2017-11-01
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary