6PPG

Crystal structure of IL17FF bound to Fab fragments of MCAF5352A

PDB DOI: https://doi.org/10.2210/pdb6PPG/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda, Cricetulus griseus
Mutation(s): No

Deposited: 2019-07-06 Released: 2019-12-11
Deposition Author(s): Huang, C.S., Yin, J.P., Hymowitz, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.275
R-Value Work: 0.224
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 131.44 kDa
Atom Count: 8,431
Modelled Residue Count: 1,103
Deposited Residue Count: 1,150
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-17F	A [auth F], F [auth G]	133	Homo sapiens	Mutation(s): 0 Gene Names: IL17F
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PD4 (Homo sapiens) Explore Q96PD4 Go to UniProtKB: Q96PD4
PHAROS: Q96PD4 GTEx: ENSG00000112116
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96PD4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab MCAF5352A light chain	B [auth A], E [auth L]	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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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab MCAF5352A heavy chain	C [auth B], D [auth H]	226	Homo sapiens	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
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain G [auth F] MOL2 format, chain CB [auth G] MOL2 format, chain G [auth F]	CB [auth G], G [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CB [auth G] Focus chain G [auth F] Interactions & Density Focus chain CB [auth G] Focus chain G [auth F]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth L] SDF format, chain BA [auth A] SDF format, chain BB [auth L] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain DB [auth G] SDF format, chain EA [auth B] SDF format, chain EB [auth G] SDF format, chain FA [auth B] SDF format, chain FB [auth G] SDF format, chain GA [auth B] SDF format, chain GB [auth G] SDF format, chain H [auth F] SDF format, chain HA [auth B] SDF format, chain HB [auth G] SDF format, chain I [auth F] SDF format, chain IA [auth B] SDF format, chain IB [auth G] SDF format, chain J [auth F] SDF format, chain JA [auth H] SDF format, chain K [auth F] SDF format, chain KA [auth H] SDF format, chain L [auth F] SDF format, chain LA [auth H] SDF format, chain M [auth A] SDF format, chain MA [auth H] SDF format, chain N [auth A] SDF format, chain NA [auth H] SDF format, chain O [auth A] SDF format, chain OA [auth H] SDF format, chain P [auth A] SDF format, chain PA [auth L] SDF format, chain Q [auth A] SDF format, chain QA [auth L] SDF format, chain R [auth A] SDF format, chain RA [auth L] SDF format, chain S [auth A] SDF format, chain SA [auth L] SDF format, chain T [auth A] SDF format, chain TA [auth L] SDF format, chain U [auth A] SDF format, chain UA [auth L] SDF format, chain V [auth A] SDF format, chain VA [auth L] SDF format, chain W [auth A] SDF format, chain WA [auth L] SDF format, chain X [auth A] SDF format, chain XA [auth L] SDF format, chain Y [auth A] SDF format, chain YA [auth L] SDF format, chain Z [auth A] SDF format, chain ZA [auth L] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth L] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth L] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth G] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth G] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth G] MOL2 format, chain H [auth F] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth G] MOL2 format, chain I [auth F] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth G] MOL2 format, chain J [auth F] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth F] MOL2 format, chain KA [auth H] MOL2 format, chain L [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth L] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth L] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth L] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth L] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth L] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth L] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth L] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth L] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth L] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth L]	AA [auth A] AB [auth L] BA [auth A] BB [auth L] CA [auth B] AA [auth A], AB [auth L], BA [auth A], BB [auth L], CA [auth B], DA [auth B], DB [auth G], EA [auth B], EB [auth G], FA [auth B], FB [auth G], GA [auth B], GB [auth G], H [auth F], HA [auth B], HB [auth G], I [auth F], IA [auth B], IB [auth G], J [auth F], JA [auth H], K [auth F], KA [auth H], L [auth F], LA [auth H], M [auth A], MA [auth H], N [auth A], NA [auth H], O [auth A], OA [auth H], P [auth A], PA [auth L], Q [auth A], QA [auth L], R [auth A], RA [auth L], S [auth A], SA [auth L], T [auth A], TA [auth L], U [auth A], UA [auth L], V [auth A], VA [auth L], W [auth A], WA [auth L], X [auth A], XA [auth L], Y [auth A], YA [auth L], Z [auth A], ZA [auth L]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth L] Focus chain BA [auth A] Focus chain BB [auth L] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth G] Focus chain EA [auth B] Focus chain EB [auth G] Focus chain FA [auth B] Focus chain FB [auth G] Focus chain GA [auth B] Focus chain GB [auth G] Focus chain H [auth F] Focus chain HA [auth B] Focus chain HB [auth G] Focus chain I [auth F] Focus chain IA [auth B] Focus chain IB [auth G] Focus chain J [auth F] Focus chain JA [auth H] Focus chain K [auth F] Focus chain KA [auth H] Focus chain L [auth F] Focus chain LA [auth H] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth L] Focus chain Q [auth A] Focus chain QA [auth L] Focus chain R [auth A] Focus chain RA [auth L] Focus chain S [auth A] Focus chain SA [auth L] Focus chain T [auth A] Focus chain TA [auth L] Focus chain U [auth A] Focus chain UA [auth L] Focus chain V [auth A] Focus chain VA [auth L] Focus chain W [auth A] Focus chain WA [auth L] Focus chain X [auth A] Focus chain XA [auth L] Focus chain Y [auth A] Focus chain YA [auth L] Focus chain Z [auth A] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth L] Focus chain BA [auth A] Focus chain BB [auth L] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth G] Focus chain EA [auth B] Focus chain EB [auth G] Focus chain FA [auth B] Focus chain FB [auth G] Focus chain GA [auth B] Focus chain GB [auth G] Focus chain H [auth F] Focus chain HA [auth B] Focus chain HB [auth G] Focus chain I [auth F] Focus chain IA [auth B] Focus chain IB [auth G] Focus chain J [auth F] Focus chain JA [auth H] Focus chain K [auth F] Focus chain KA [auth H] Focus chain L [auth F] Focus chain LA [auth H] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth L] Focus chain Q [auth A] Focus chain QA [auth L] Focus chain R [auth A] Focus chain RA [auth L] Focus chain S [auth A] Focus chain SA [auth L] Focus chain T [auth A] Focus chain TA [auth L] Focus chain U [auth A] Focus chain UA [auth L] Focus chain V [auth A] Focus chain VA [auth L] Focus chain W [auth A] Focus chain WA [auth L] Focus chain X [auth A] Focus chain XA [auth L] Focus chain Y [auth A] Focus chain YA [auth L] Focus chain Z [auth A] Focus chain ZA [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.275
R-Value Work: 0.224
R-Value Observed: 0.227
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.82	α = 90
b = 103.82	β = 90
c = 243.327	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-12-11

Deposition Author(s):

Huang, C.S.

Yin, J.P.

Hymowitz, S.G.

Revision History (Full details and data files)

Version 1.0: 2019-12-11
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary