SMTL ID : 9h0m.2 (1 other biounit)

Structure of avian Pit54 SRCR 1-2 in complex with hemoglobin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

hetero-2-2-2-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain E: E.205, N.245, Q.257 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.245

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

HEM.2: 17 residues within 4Å: Chain A: 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 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.43, A:F.44, A:K.62, A:K.62, A:A.66, A:L.84, A:L.87, A:L.92, A:V.94, A:N.98, A:F.99, A:L.102, A:L.137 Salt bridges: A:H.46, A:K.62 pi-Stacking: A:F.99 Metal complexes: A:H.88 HEM.3: 20 residues within 4Å: Chain B: L.32, T.39, F.42, F.43, F.46, H.64, K.67, V.68, S.71, F.72, L.89, H.93, L.97, V.99, N.103, F.104, L.107, L.142 Chain E: R.234, Y.267 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain E, Hydrophobic interactions: B:L.32, B:T.39, B:F.42, B:F.42, B:F.43, B:V.68, B:F.72, B:F.72, B:L.89, B:L.89, B:L.97, B:V.99, B:V.99, B:N.103, B:F.104, B:L.107, B:L.142 pi-Stacking: B:H.64 Metal complexes: B:H.93 Hydrogen bonds: E:R.234 Salt bridges: E:R.234 HEM.4: 17 residues within 4Å: Chain C: 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, N.98, F.99, L.102, L.137 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:Y.43, C:Y.43, C:F.47, C:K.62, C:K.62, C:V.63, C:A.66, C:L.84, C:L.87, C:L.92, C:N.98, C:L.102, C:L.137 Salt bridges: C:H.46 Metal complexes: C:H.88 HEM.5: 22 residues within 4Å: Chain D: T.39, F.42, F.43, F.46, H.64, K.67, V.68, S.71, F.72, F.86, L.89, L.92, H.93, L.97, V.99, N.103, F.104, L.107, V.138, L.142 Chain F: R.234, Y.267 23 PLIP interactions: 21 interactions with chain D, 2 interactions with chain F, Hydrophobic interactions: D:T.39, D:F.42, D:F.42, D:F.43, D:F.43, D:V.68, D:F.72, D:F.72, D:F.86, D:L.89, D:L.89, D:L.92, D:L.97, D:V.99, D:N.103, D:F.104, D:L.107, D:V.138, D:L.142 pi-Stacking: D:H.64 Metal complexes: D:H.93 Hydrogen bonds: F:R.234 Salt bridges: F:R.234

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain E: G.95, D.97, R.99, E.100, L.134, D.135 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:G.95, E:D.97, E:E.100, E:E.100 CA.7: 4 residues within 4Å: Chain E: D.204, D.242, D.243, N.265 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.204, E:D.242, E:D.243 CA.8: 6 residues within 4Å: Chain F: G.95, D.97, R.99, E.100, L.134, D.135 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:G.95, F:D.97, F:E.100, F:L.134 CA.9: 4 residues within 4Å: Chain F: D.204, D.242, D.243, N.265 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.204, F:D.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikkelsen, J.H. et al., Structure of avian Pit54 SRCR 1-2 in complex with hemoglobin. To Be Published

Release Date

2025-10-29

Peptides

Hemoglobin subunit alpha-A: AC
Hemoglobin subunit beta: BD
PIT54 protein: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
I

B
H

D
J

E
K

F
L

Hemoglobin subunit alpha-A

Hemoglobin subunit beta

PIT54 protein

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