8Q6R

Structure of complement FP in complex with the TPP-3077 VHH

PDB DOI: https://doi.org/10.2210/pdb8Q6R/pdb

Classification: IMMUNE SYSTEM
Organism(s): Lama glama, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-14 Released: 2024-08-28
Deposition Author(s): Andersen, G.R., Pedersen, D.V.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238
R-Value Work: 0.202
R-Value Observed: 0.203

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of complement FP in complex with the TPP-3077 VHH

Andersen, G.R., Pedersen, D.V.

To be published.

Macromolecule Content

Total Structure Weight: 107.27 kDa
Atom Count: 7,492
Modelled Residue Count: 875
Deposited Residue Count: 908
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
The properdin specific VHH TPP-3077	A, B	125	Lama glama	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Properdin	C, E	108	Homo sapiens	Mutation(s): 0 Gene Names: CFP
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens) Explore P27918 Go to UniProtKB: P27918
PHAROS: P27918 GTEx: ENSG00000126759
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27918
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C Focus chain E	Go to GlyGen: P27918-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Properdin	D, F	221	Homo sapiens	Mutation(s): 0 Gene Names: CFP
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens) Explore P27918 Go to UniProtKB: P27918
PHAROS: P27918 GTEx: ENSG00000126759
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27918
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain D Focus chain F	Go to GlyGen: P27918-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose	G, H, J, K	2		O-Glycosylation	Interactions Focus chain G Focus chain H Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G36855WW GlyCosmos: G36855WW GlyGen: G36855WW

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	2		N-Glycosylation	Interactions Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCH (Subject of Investigation/LOI) Query on GCH Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A]	L [auth A], M [auth A]	GLYCOCHOLIC ACID C₂₆ H₄₃ N O₆ RFDAIACWWDREDC-FRVQLJSFSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth F] MOL2 format, chain DA [auth F]	DA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth F]
MAN (Subject of Investigation/LOI) Query on MAN Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain Q [auth D] SDF format, chain T [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth D]	AA [auth F] BA [auth F] CA [auth F] EA [auth F] FA [auth F] AA [auth F], BA [auth F], CA [auth F], EA [auth F], FA [auth F], GA [auth F], HA [auth F], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth D], V [auth D], W [auth D], X [auth E], Y [auth E], Z [auth F]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth F]