6QKD

CRYSTAL STRUCTURE OF vhh-based FAB-fragment of antibody BCD-085

PDB DOI: https://doi.org/10.2210/pdb6QKD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Lama glama
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2019-01-29 Released: 2019-07-24
Deposition Author(s): Kostareva, O.S., Kolyadenko, I.A., Ulitin, A.B., Ekimova, V.M., Evdokimov, S.R., Garber, M.B., Tishchenko, T.V., Gabdulkhakov, A.G.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.228
R-Value Work: 0.169
R-Value Observed: 0.172

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Fab Fragment of VHH-Based Antibody Netakimab: Crystal Structure and Modeling Interaction with Cytokine IL-17A

Kostareva, O.S., Kolyadenko, I.A., Ulitin, A.B., Ekimova, V.M., Evdokimov, S.R., Garber, M.B., Tishchenko, T.V., Gabdulkhakov, A.G.

(2019) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst9030177

Macromolecule Content

Total Structure Weight: 190.79 kDa
Atom Count: 13,541
Modelled Residue Count: 1,742
Deposited Residue Count: 1,772
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB HEAVY CHAIN	A [auth H], B [auth I], C [auth J], D [auth K]	228	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB LIGHT CHAIN	E [auth L], F [auth M], G [auth O], H [auth T]	215	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain J [auth I] SDF format, chain L [auth K] SDF format, chain M [auth K] SDF format, chain O [auth L] SDF format, chain P [auth L] SDF format, chain Q [auth M] SDF format, chain R [auth M] SDF format, chain S [auth O] SDF format, chain T MOL2 format, chain I [auth H] MOL2 format, chain J [auth I] MOL2 format, chain L [auth K] MOL2 format, chain M [auth K] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain S [auth O] MOL2 format, chain T mmCIF format, chain I [auth H] mmCIF format, chain J [auth I] mmCIF format, chain L [auth K] mmCIF format, chain M [auth K] mmCIF format, chain O [auth L] mmCIF format, chain P [auth L] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M] mmCIF format, chain S [auth O] mmCIF format, chain T	I [auth H] J [auth I] L [auth K] M [auth K] O [auth L] I [auth H], J [auth I], L [auth K], M [auth K], O [auth L], P [auth L], Q [auth M], R [auth M], S [auth O], T	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth H] Focus chain J [auth I] Focus chain L [auth K] Focus chain M [auth K] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth O] Focus chain T Interactions & Density Focus chain I [auth H] Focus chain J [auth I] Focus chain L [auth K] Focus chain M [auth K] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth O] Focus chain T
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth I] SDF format, chain N [auth K] SDF format, chain U [auth T] MOL2 format, chain K [auth I] MOL2 format, chain N [auth K] MOL2 format, chain U [auth T] mmCIF format, chain K [auth I] mmCIF format, chain N [auth K] mmCIF format, chain U [auth T]	K [auth I], N [auth K], U [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth I] Focus chain N [auth K] Focus chain U [auth T] Interactions & Density Focus chain K [auth I] Focus chain N [auth K] Focus chain U [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.228
R-Value Work: 0.169
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.56	α = 90
b = 111.92	β = 90
c = 165.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	17-74-10156

Revision History (Full details and data files)

Version 1.0: 2019-07-24
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary