Structural basis for iron piracy by pathogenic Neisseria.

Noinaj, N; Easley, N.C; Oke, M; Mizuno, N; Gumbart, J; Boura, E; Steere, A.N; Zak, O; Aisen, P; Tajkhorshid, E; Evans, R.W; Gorringe, A.R; Mason, A.B; Steven, A.C; Buchanan, S.K.

Macromolecule Content

Unique protein chains: 2

3V8X

The crystal structure of transferrin binding protein A (TbpA) from Neisserial meningitidis serogroup B in complex with full length human transferrin

DOI: 10.2210/pdb3v8x/pdb

Classification: MEMBRANE PROTEIN / METAL TRANSPORT
Deposited: 2011-12-23 Released: 2012-02-29
Deposition author(s): Noinaj, N., Easley, N., Buchanan, S.K.
Organism: Neisseria meningitidis | Homo sapiens
Expression System: Escherichia coli
Mutation(s): 3

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.6 Å
R-Value Free: 0.267
R-Value Work: 0.208

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: MEMBRANE PROTEIN / METAL TRANSPORT

Total Structure Weight: 182684.78

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
Transferrin-binding protein 1	A	904	Neisseria meningitidis	Mutation: I435V, M913Y Gene Name(s): tbp1 NMB0461
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: Q9K0U9 UniProt Full Protein Feature View for Q9K0U9 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for Q9K0U9/3V8X
Serotransferrin	B	698	Homo sapiens	Mutation: I429V Gene Name(s): TF Gene View PRO1400
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: P02787 UniProt Full Protein Feature View for P02787 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for P02787/3V8X

Membrane Protein

Source: mpstruc | Group: BETA-BARREL

Subgroup Name: Beta-Barrel Membrane Proteins: Monomeric/Dimeric

Protein Name: Transferrin binding protein A (TbpA) in complex with human transferrin

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
SIA Query on SIA Download SDF File Download CCD File	B	O-SIALIC ACID C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N	Poseview Image of SIA in 3V8X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
C8E Query on C8E Download SDF File Download CCD File	A	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N	Poseview Image of C8E in 3V8X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
NAG Query on NAG Download SDF File Download CCD File	B	N-ACETYL-D-GLUCOSAMINE C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N	Poseview Image of NAG in 3V8X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
GAL Query on GAL Download SDF File Download CCD File	B	BETA-D-GALACTOSE C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N	Poseview Image of GAL in 3V8X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
MAN Query on MAN Download SDF File Download CCD File	B	ALPHA-D-MANNOSE C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N	Poseview Image of MAN in 3V8X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
BMA Query on BMA Download SDF File Download CCD File	B	BETA-D-MANNOSE C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N	Poseview Image of BMA in 3V8X Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)