SMTL ID : 7jrd.1

The crystal structure of lactoferrin binding protein B (LbpB) from Neisseria meningitidis in complex with human lactoferrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: D.396, Y.436, Y.529, H.598 Ligands: BCT.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.396, A:Y.436, A:Y.529, A:H.598 FE.2: 7 residues within 4Å: Chain A: D.61, Y.93, R.122, T.123, Y.193, H.254 Ligands: BCT.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.61, A:Y.93, A:Y.193, A:H.254

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.3: 10 residues within 4Å: Chain A: D.396, Y.436, T.462, R.466, T.467, A.468, G.469, Y.529, H.598 Ligands: FE.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.462, A:R.466, A:T.467, A:A.468, A:G.469 BCT.4: 10 residues within 4Å: Chain A: D.61, Y.93, T.118, R.122, T.123, A.124, G.125, W.126, Y.193 Ligands: FE.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.118, A:A.124

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: R.444, T.447, R.581 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.444, A:R.581 SO4.6: 1 residues within 4Å: Chain A: N.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.169 SO4.7: 2 residues within 4Å: Chain A: R.609 Chain B: T.286 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.286 Salt bridges: A:R.609 SO4.8: 3 residues within 4Å: Chain A: I.38, R.40, R.54 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.40 SO4.9: 3 residues within 4Å: Chain A: H.591, A.593, M.594 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.594 Salt bridges: A:H.591 SO4.10: 2 residues within 4Å: Chain A: R.76, R.314 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.76, A:R.314 SO4.11: 5 residues within 4Å: Chain A: R.90, T.91, H.92, R.250, K.692 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.91, A:T.91, A:H.92 Salt bridges: A:R.250 SO4.12: 1 residues within 4Å: Chain A: R.333 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.333 SO4.13: 5 residues within 4Å: Chain A: R.466, Y.527, G.528, Y.529, N.641 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.529, A:N.641 Salt bridges: A:R.466 SO4.14: 3 residues within 4Å: Chain A: K.405, Y.660, R.691 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.660 Salt bridges: A:K.405, A:R.691 SO4.15: 2 residues within 4Å: Chain B: R.56, R.110 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.56, B:R.110 SO4.16: 3 residues within 4Å: Chain B: K.104, N.108, V.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.108 SO4.17: 1 residues within 4Å: Chain B: K.269 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, R. et al., Structural insight into the dual function of LbpB in mediating Neisserial pathogenesis. Elife (2021)

Release Date

2021-10-13

Peptides

Lactotransferrin: A
Lactoferrin-binding protein B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Lactotransferrin

Lactoferrin-binding protein B

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