SMTL ID : 6r2o.1

Hemoglobin structure from serial crystallography with a 3D-printed nozzle.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: M.32, T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.129, V.132, L.136 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:Y.42, A:F.43, A:F.43, A:K.61, A:V.62, A:L.91, A:V.93, A:L.101, A:L.136 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58 Metal complexes: A:H.87 HEM.3: 22 residues within 4Å: Chain B: L.31, T.38, F.41, F.42, F.45, H.63, K.66, V.67, S.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, V.137, A.138, L.141 23 PLIP interactions: 22 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:F.42, B:F.71, B:F.71, B:L.88, B:L.96, B:L.96, B:V.98, B:V.98, B:N.102, B:F.103, B:L.106, B:V.137, B:L.141 Salt bridges: B:K.66 pi-Stacking: B:H.63, B:H.63 Metal complexes: B:H.92, H2O.1 HEM.4: 22 residues within 4Å: Chain C: M.32, T.39, Y.42, F.43, H.45, F.46, H.58, K.61, V.62, A.65, L.66, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.129, V.132, L.136 18 PLIP interactions: 17 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:F.43, C:L.86, C:L.91, C:V.93, C:F.98, C:L.101, C:V.132, C:L.136 Water bridges: C:H.58 Salt bridges: C:H.45, C:K.61 pi-Stacking: C:H.58, C:H.58 Metal complexes: C:H.87, H2O.1 HEM.7: 22 residues within 4Å: Chain D: L.31, T.38, F.41, F.42, F.45, H.63, K.66, V.67, S.70, F.71, F.85, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, G.107, V.137, L.141 21 PLIP interactions: 20 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:V.67, D:F.71, D:L.88, D:L.88, D:L.91, D:L.96, D:V.98, D:N.102, D:F.103, D:L.106, D:L.141 Salt bridges: D:K.66 pi-Stacking: D:H.63 Metal complexes: D:H.92, H2O.2

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: H.103, L.106 Chain B: N.108, V.112 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.102, A:D.126 NA.5: 6 residues within 4Å: Chain C: L.106, H.122 Chain D: V.34, Y.35, V.109, V.112 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.35, C:H.122

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain C: T.118, P.119, A.120 Chain D: P.51 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 3 residues within 4Å: Chain D: E.90, D.94, K.95 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knoska, J. et al., Ultracompact 3D microfluidics for time-resolved structural biology. Nat Commun (2020)

Release Date

2020-01-29

Peptides

Hemoglobin subunit alpha: AC
Hemoglobin subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hemoglobin subunit alpha

Hemoglobin subunit beta

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