SMTL ID : 9hba.1

Crystal structure of C35 bound to Hem

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

hetero-2-2-mer

Ligands

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

HEM.1: 18 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 Ligands: CMO.6 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.42, A:Y.42, A:Y.42, A:F.43, A:K.61, A:L.66, A:L.83, A:L.91, A:V.93, A:F.98, A:L.101, A:L.136 Water bridges: A:H.58 Salt bridges: A:H.45, A:K.61 pi-Stacking: A:H.58, A:H.87 Metal complexes: A:H.87 HEM.15: 19 residues within 4Å: Chain B: T.38, F.41, F.42, F.45, H.63, K.66, A.70, F.71, L.88, L.91, H.92, L.96, V.98, N.102, F.103, L.106, L.141 Ligands: CMO.19, PGE.20 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:T.38, B:F.41, B:F.41, B:F.42, B:F.42, B:F.71, B:F.71, B:L.88, B:L.91, B:L.96, B:V.98, B:N.102, B:F.103, B:L.106, B:L.141 Water bridges: B:H.63 Salt bridges: B:H.63, B:K.66 pi-Cation interactions: B:H.92 Metal complexes: B:H.92 HEM.32: 15 residues within 4Å: Chain C: Y.42, F.43, H.58, K.61, A.65, L.83, L.86, H.87, L.91, V.93, N.97, F.98, L.101, L.136 Ligands: CMO.33 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:Y.42, C:Y.42, C:F.43, C:L.83, C:L.91, C:V.93, C:F.98, C:L.136 Salt bridges: C:H.45, C:K.61, C:K.61 pi-Stacking: C:H.58, C:H.58 Metal complexes: C:H.87 HEM.39: 18 residues within 4Å: Chain D: 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 Ligands: CMO.40 18 PLIP interactions: 17 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:T.38, D:F.41, D:F.41, D:F.42, D:F.42, D:V.67, D:F.71, D:L.88, 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, CMO.40

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: D.74, P.77 Ligands: 01.3, 01.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.74 Water bridges: A:D.75 GOL.7: 7 residues within 4Å: Chain A: F.98, K.99, S.102, D.126, L.129, A.130, S.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.102, A:D.126, A:A.130, A:S.133, A:S.133 GOL.21: 5 residues within 4Å: Chain B: L.78, D.79, N.80, L.81, K.82 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.78, B:L.81, B:K.82 GOL.31: 8 residues within 4Å: Chain A: V.1, K.127, A.130 Chain C: T.137, S.138 Ligands: ACY.8, DMS.9, DMS.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.137, C:T.137, A:K.127 GOL.35: 7 residues within 4Å: Chain C: F.98, K.99, S.102, D.126, L.129, A.130, S.133 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.102, C:D.126, C:S.133, C:S.133 GOL.44: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x 01: 4-[2-[[5-(1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl]ethanoylamino]benzoic acid

01.3: 16 residues within 4Å: Chain A: V.1, L.2, K.7, V.73, D.74, S.131 Chain C: P.77, N.78, S.131, V.135, Y.140, R.141 Ligands: GOL.2, ACY.8, 01.30, ACY.34 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:V.1, A:V.1, C:P.77, C:V.135, C:Y.140 Hydrogen bonds: A:V.1, A:L.2 Water bridges: C:N.78 Salt bridges: C:R.141 01.17: 2 residues within 4Å: Chain B: K.95, L.96 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.95, B:L.96 01.30: 16 residues within 4Å: Chain A: P.77, N.78, S.131, V.135, Y.140, R.141 Chain C: V.1, L.2, K.7, V.73, D.74, S.131 Ligands: GOL.2, 01.3, ACY.8, ACY.34 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:P.77, A:V.135, A:Y.140, C:V.1, C:V.1 Water bridges: A:M.76, A:N.78 Salt bridges: A:R.141 Hydrogen bonds: C:V.1, C:L.2

8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 3 residues within 4Å: Chain A: H.89, K.139, R.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.139 Water bridges: A:H.89 DMS.5: 6 residues within 4Å: Chain A: A.26, E.27, E.30, H.50, G.51, K.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.51 Salt bridges: A:E.30 DMS.9: 7 residues within 4Å: Chain A: K.127 Chain B: P.36 Chain C: T.137, S.138, K.139 Ligands: DMS.14, GOL.31 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:K.127, A:K.127 Hydrogen bonds: C:K.139 DMS.14: 7 residues within 4Å: Chain A: D.126, A.130 Chain B: V.34, Y.35, W.37 Ligands: DMS.9, GOL.31 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.126 DMS.16: 7 residues within 4Å: Chain B: G.25, E.26, V.54, M.55, N.57, V.60, K.61 No protein-ligand interaction detected (PLIP) DMS.18: 1 residues within 4Å: Chain B: K.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.59 DMS.22: 3 residues within 4Å: Chain B: W.15, S.72, L.75 No protein-ligand interaction detected (PLIP) DMS.41: 9 residues within 4Å: Chain A: K.139 Chain D: L.32, V.33, Q.39, L.48, S.49, T.50, P.51, V.54 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.39, A:K.139

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.6: 5 residues within 4Å: Chain A: L.29, F.43, H.58, V.62 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.58 CMO.19: 6 residues within 4Å: Chain B: L.28, F.42, H.63, V.67, H.92 Ligands: HEM.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.63 CMO.33: 5 residues within 4Å: Chain C: L.29, H.58, V.62, H.87 Ligands: HEM.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.58 CMO.40: 4 residues within 4Å: Chain D: F.42, H.63, V.67 Ligands: HEM.39 No protein-ligand interaction detected (PLIP)

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.8: 9 residues within 4Å: Chain A: V.1, A.130, S.131, T.134 Chain C: T.134 Ligands: 01.3, 01.30, GOL.31, ACY.34 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.134 Hydrogen bonds: A:V.1, A:T.134, A:T.134 ACY.34: 8 residues within 4Å: Chain A: T.134 Chain C: V.1, A.130, S.131, T.134 Ligands: 01.3, ACY.8, 01.30 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.134 Hydrogen bonds: C:V.1

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

SO4.10: 5 residues within 4Å: Chain A: A.71, H.72, V.73, D.74, D.75 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: K.11, A.71 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: W.14, G.15, G.18, T.67 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: H.20, Y.24, H.112 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: H.2, T.4, K.132 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain B: P.100, R.104, H.146 Chain D: R.104, H.146 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain A: S.35, F.36 Chain B: Q.131, K.132, A.135 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain A: P.114 Chain B: H.116, H.117 Ligands: SO4.27, SO4.28 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain A: P.114 Chain B: H.116, H.117, G.119 Ligands: SO4.26 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain A: P.119 Chain B: E.26, R.30, M.55, H.116 Ligands: SO4.26 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: W.15, V.18, V.20, S.72 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain C: A.5, N.9 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain C: S.35, F.36 Chain D: Q.131, A.135 Ligand excluded by PLIP SO4.38: 7 residues within 4Å: Chain C: A.26, E.27, E.30, H.50, G.51, S.52, K.56 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain D: L.78, D.79, N.80, L.81, K.82 Ligand excluded by PLIP SO4.43: 5 residues within 4Å: Chain B: Y.145, H.146 Chain D: A.135, G.136, N.139 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.20: 4 residues within 4Å: Chain B: D.73, T.87, L.88 Ligands: HEM.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.73 Water bridges: B:L.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marchesani, F. et al., Crystal structure of C35 bound to Hem. To Be Published

Release Date

2025-11-19

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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