SMTL ID : 9bcj.1

Crystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Chain C: L.94, G.95, Y.96, G.97, L.170 22 PLIP interactions: 16 interactions with chain A, 5 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: A:Y.42, A:Y.42, A:F.43, A:F.43, A:L.83, A:L.91, A:V.93, A:F.98, A:F.98, A:L.101, A:L.136, C:Y.96, C:L.170 Water bridges: A:H.58, C:G.97, C:G.97 Salt bridges: A:H.45, A:H.58, A:K.61 Metal complexes: A:H.87, H2O.2 Hydrogen bonds: C:Y.96 HEM.3: 17 residues within 4Å: Chain B: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:V.67, B:F.71, B:L.91, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Water bridges: B:K.66 Salt bridges: B:K.66 pi-Stacking: B:H.63 Metal complexes: B:H.92, H2O.5 HEM.7: 22 residues within 4Å: Chain D: Y.42, F.43, H.45, F.46, H.58, K.61, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Chain F: L.94, G.95, Y.96, G.97, L.170 22 PLIP interactions: 16 interactions with chain D, 5 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: D:Y.42, D:Y.42, D:F.43, D:F.43, D:L.83, D:L.91, D:V.93, D:F.98, D:F.98, D:L.101, D:L.136, F:Y.96, F:L.170 Water bridges: D:H.58, F:G.97, F:G.97 Salt bridges: D:H.45, D:H.58, D:K.61 Metal complexes: D:H.87, H2O.12 Hydrogen bonds: F:Y.96 HEM.9: 17 residues within 4Å: Chain E: T.38, F.41, F.42, H.63, K.66, V.67, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 20 PLIP interactions: 19 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:T.38, E:F.41, E:F.41, E:F.42, E:F.42, E:V.67, E:F.71, E:L.91, E:L.96, E:V.98, E:N.102, E:F.103, E:L.106, E:L.141 Water bridges: E:H.63, E:K.66 Salt bridges: E:K.66 pi-Stacking: E:H.63 Metal complexes: E:H.92, H2O.16

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: P.95, T.134, T.137, S.138 Chain B: W.37 Chain D: K.127 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.137 Water bridges: A:T.134, A:T.134, A:T.137, D:V.1 GOL.4: 3 residues within 4Å: Chain B: A.135 Chain D: S.35, F.36 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.35 Water bridges: B:A.135 GOL.6: 10 residues within 4Å: Chain C: G.12, S.17, H.18, P.26, K.27, F.28, R.60, D.64, I.65, L.66 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:G.12, C:F.28, C:R.60, C:L.66 Water bridges: C:D.64, C:D.64 GOL.8: 6 residues within 4Å: Chain A: K.127 Chain D: P.95, T.134, T.137, S.138 Chain E: W.37 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.137 Water bridges: D:T.134, D:T.134, D:T.137 GOL.10: 3 residues within 4Å: Chain A: S.35, F.36 Chain E: A.135 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Water bridges: E:A.135 Hydrogen bonds: A:S.35 GOL.12: 10 residues within 4Å: Chain F: G.12, S.17, H.18, P.26, K.27, F.28, R.60, D.64, I.65, L.66 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.12, F:F.28, F:R.60, F:L.66 Water bridges: F:D.64, F:D.64

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 8 residues within 4Å: Chain A: K.139 Chain B: P.36, Q.39, L.48, S.49, T.50, P.51, V.54 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.39, B:Q.39 Water bridges: A:K.139, A:K.139, A:K.139 Salt bridges: A:K.139 PO4.11: 8 residues within 4Å: Chain D: K.139 Chain E: P.36, Q.39, L.48, S.49, T.50, P.51, V.54 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Water bridges: D:K.139, D:K.139, D:K.139 Salt bridges: D:K.139 Hydrogen bonds: E:Q.39, E:Q.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mahoney, B.J. et al., Molecular basis of hemoglobin binding and heme removal in Corynebacterium diphtheriae. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-01-08

Peptides

Hemoglobin subunit alpha: AD
Hemoglobin subunit beta: BE
Membrane protein: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
C

F
C

Hemoglobin subunit alpha

Hemoglobin subunit beta

Membrane protein

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