SMTL ID : 4myp.1

Structure of the central NEAT domain, N2, of the listerial Hbp2 protein complexed with heme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 14 residues within 4Å: Chain A: K.16, S.23, S.24, M.25, Y.28, Y.99, A.101, F.103, Y.108, A.112 Chain B: S.24, F.103 Ligands: GOL.7, HEM.10 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:Y.28, A:Y.99, A:Y.99, A:Y.99, A:F.103, A:Y.108, A:Y.108, A:A.112, B:F.103 Hydrogen bonds: A:S.24 Water bridges: A:D.113 Salt bridges: A:K.16 pi-Stacking: A:Y.99, B:F.103 Metal complexes: A:Y.99 HEM.10: 15 residues within 4Å: Chain A: K.16, S.24 Chain B: K.16, S.23, S.24, M.25, Y.28, T.53, Y.99, A.101, F.103, Y.108, A.112 Ligands: HEM.1, GOL.15 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:Y.28, B:T.53, B:Y.99, B:Y.99, B:Y.99, B:A.101, B:F.103, B:Y.108, B:Y.108, B:A.112 Hydrogen bonds: B:S.24 Water bridges: B:D.113 Salt bridges: B:K.16 pi-Stacking: B:Y.99, B:Y.108 Metal complexes: B:Y.99

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.96, D.113 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.96, A:D.113, A:D.113, H2O.1 ZN.3: 2 residues within 4Å: Chain A: D.74, D.76 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.74 ZN.4: 1 residues within 4Å: Chain A: D.76 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.76, H2O.1 ZN.11: 2 residues within 4Å: Chain B: H.96, D.113 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.96, B:D.113, B:D.113, H2O.3

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: N.30, P.32, M.46, T.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.30, A:T.47 Water bridges: A:N.31 GOL.6: 6 residues within 4Å: Chain A: T.2, K.42, E.87, D.88, L.89, N.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.2, A:T.2, A:L.89, A:N.90 GOL.7: 5 residues within 4Å: Chain A: Y.99, Y.108, G.110, Q.111 Ligands: HEM.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.99, A:Q.111, A:Q.111 GOL.8: 5 residues within 4Å: Chain A: P.11, F.12, V.13, N.31, D.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.12, A:N.31, A:D.119 GOL.9: 5 residues within 4Å: Chain A: N.22, S.23, S.24, Q.26, N.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.22, A:N.27 GOL.12: 5 residues within 4Å: Chain A: F.103 Chain B: N.27, Y.28, N.49, D.50 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.27, B:N.49, B:D.50 Water bridges: B:D.50, B:T.53 GOL.13: 4 residues within 4Å: Chain B: E.73, D.74, K.75, D.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.74, B:K.75, B:D.76 GOL.14: 2 residues within 4Å: Chain B: H.96, Q.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.111 GOL.15: 5 residues within 4Å: Chain B: Y.99, Y.108, G.110, Q.111 Ligands: HEM.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.99, B:Y.108, B:Q.111, B:Q.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malmirchegini, G.R. et al., Novel Mechanism of Hemin Capture by Hbp2, the Hemoglobin-binding Hemophore from Listeria monocytogenes. J.Biol.Chem. (2014)

Release Date

2014-10-22

Peptides

Iron-regulated surface determinant protein A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Iron-regulated surface determinant protein A

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