SMTL ID : 8vyl.1

The structure of Human Hemoglobin in Complex with Nanobody BtNbE11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 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: M.33, T.40, Y.43, F.44, F.47, H.59, K.62, V.63, A.66, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.130, V.133, L.137 Ligands: ACE.2 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:Y.43, A:F.44, A:K.62, A:V.63, A:A.66, A:L.84, A:L.84, A:L.92, A:V.94, A:F.99, A:F.99, A:L.102, A:V.133, A:L.137 Salt bridges: A:K.62, A:K.62 pi-Stacking: A:H.59, A:H.59 Metal complexes: A:H.88, H2O.1 HEM.3: 17 residues within 4Å: Chain B: Y.43, F.44, F.47, H.59, K.62, V.63, A.66, L.67, L.84, L.87, H.88, L.92, V.94, N.98, F.99, L.102, L.137 17 PLIP interactions: 16 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:Y.43, B:F.44, B:F.47, B:V.63, B:A.66, B:L.84, B:L.92, B:V.94, B:F.99, B:L.102, B:L.102, B:L.137 Water bridges: B:K.62 Salt bridges: B:K.62 pi-Stacking: B:H.59 Metal complexes: B:H.88, H2O.5 HEM.4: 17 residues within 4Å: Chain C: T.39, F.42, F.43, 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, L.142 18 PLIP interactions: 17 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:T.39, C:F.42, C:F.42, C:F.43, C:F.43, C:V.68, C:V.68, C:A.71, C:L.89, C:L.97, C:V.99, C:F.104, C:L.107, C:L.142 Water bridges: C:S.45, C:K.67 Metal complexes: C:H.93, H2O.8 HEM.5: 15 residues within 4Å: Chain D: T.39, F.42, F.43, H.64, K.67, V.68, A.71, L.89, H.93, L.97, V.99, N.103, F.104, L.107, L.142 20 PLIP interactions: 19 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:T.39, D:F.42, D:F.42, D:F.43, D:F.43, D:V.68, D:A.71, D:L.89, D:L.97, D:V.99, D:V.99, D:N.103, D:L.107, D:L.142 Water bridges: D:H.64, D:K.67 Salt bridges: D:K.67 pi-Stacking: D:H.64 Metal complexes: D:H.93, H2O.12

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.2: 6 residues within 4Å: Chain A: Y.43, F.44, P.45, H.46, F.47 Ligands: HEM.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.46, A:H.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fox, D.R. et al., The structure of a haemoglobin-nanobody complex reveals human beta-subunit-specific interactions. Febs Lett. (2024)

Release Date

2024-07-17

Peptides

Hemoglobin subunit alpha: AB
Hemoglobin subunit beta: CD
Nanobody BtNbE11: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

E
F

F
E

Hemoglobin subunit alpha

Hemoglobin subunit beta

Nanobody BtNbE11

Related Entries With Identical Sequence