SMTL ID : 7cue.1

Crystal structure of HID2 bound to human Hemoglobin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-2-2-3-mer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: M.33, Y.43, F.44, H.46, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 Chain E: R.26, Y.27, N.67, M.68 25 PLIP interactions: 18 interactions with chain A, 6 interactions with chain E, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.44, A:F.44, A:V.63, A:L.84, A:L.84, A:L.87, A:L.92, A:V.94, A:F.99, A:F.99, A:L.102, A:L.137, E:Y.27 Salt bridges: A:H.46, A:H.59, A:K.62, E:R.26 pi-Stacking: A:H.59 pi-Cation interactions: A:H.88 Metal complexes: A:H.88, H2O.1 Hydrogen bonds: E:Y.27, E:Y.27, E:Y.27, E:M.68 HEM.2: 23 residues within 4Å: Chain B: T.39, F.42, F.43, F.46, H.64, K.67, V.68, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, V.138, L.142 Chain F: R.26, Y.27, N.67, M.68 24 PLIP interactions: 18 interactions with chain B, 5 interactions with chain F, 1 Ligand-Water interactions, Hydrophobic interactions: B:T.39, B:F.42, B:F.42, B:F.43, B:F.43, B:F.43, B:V.68, B:F.72, B:L.89, B:L.92, B:L.97, B:V.99, B:V.138, B:L.142, F:Y.27 Salt bridges: B:H.64, B:K.67, F:R.26 pi-Stacking: B:H.64 Metal complexes: B:H.93, H2O.1 Hydrogen bonds: F:Y.27, F:Y.27, F:M.68 HEM.4: 17 residues within 4Å: Chain C: Y.43, F.44, F.47, H.59, K.62, V.63, A.66, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, V.133, L.137 20 PLIP interactions: 19 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:F.44, C:V.63, C:V.63, C:A.66, C:L.84, C:L.87, C:L.92, C:V.94, C:N.98, C:F.99, C:F.99, C:L.102, C:V.133, C:L.137 Salt bridges: C:H.59, C:K.62 pi-Stacking: C:H.59 pi-Cation interactions: C:H.88 Metal complexes: C:H.88, H2O.1 HEM.5: 22 residues within 4Å: Chain D: T.39, F.42, F.43, F.46, H.64, K.67, A.71, F.72, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, V.138, L.142 Chain G: R.26, Y.27, N.67, M.68 23 PLIP interactions: 18 interactions with chain D, 4 interactions with chain G, 1 Ligand-Water interactions, Hydrophobic interactions: D:F.42, D:F.42, D:F.43, D:F.43, D:F.43, D:F.72, D:L.89, D:L.92, D:L.97, D:V.99, D:N.103, D:V.138, D:L.142, G:Y.27 Salt bridges: D:H.64, D:K.67, G:R.26 pi-Stacking: D:H.64, D:H.93 Metal complexes: D:H.93, H2O.1 Hydrogen bonds: G:Y.27, G:M.68

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

SO4.3: 2 residues within 4Å: Chain B: K.83, H.144 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.83, B:H.144 SO4.6: 4 residues within 4Å: Chain B: F.42, S.45 Chain F: K.34, Q.38 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Q.38, B:S.45 Salt bridges: F:K.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caaveiro, J.M.M. et al., Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes. To Be Published

Release Date

2021-07-07

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD
Amino acid ABC transporter substrate-binding protein: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

G
H

Hemoglobin subunit alpha

Hemoglobin subunit beta

Amino acid ABC transporter substrate-binding protein

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