SMTL ID : 3wfw.1

Crystal Structure of the Closed Form of the HGbRL's Globin Domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 18 residues within 4Å: Chain A: L.77, R.80, H.81, Y.84, V.86, H.90, Y.91, V.94, Y.122, L.125, M.129 Chain B: L.41, F.42, I.46, K.52, D.55, V.56, W.59 21 PLIP interactions: 14 interactions with chain A, 7 interactions with chain B, Hydrophobic interactions: A:L.77, A:L.77, A:Y.84, A:Y.84, A:V.86, A:V.86, A:H.90, A:Y.91, A:V.94, A:Y.122, B:L.41, B:L.41, B:F.42, B:D.55, B:V.56, B:W.59 Hydrogen bonds: A:Y.84, A:Y.84 Salt bridges: A:R.80 Metal complexes: A:H.81 Water bridges: B:R.51 HEM.4: 18 residues within 4Å: Chain A: L.41, F.42, I.46, K.52, D.55, V.56, W.59 Chain B: L.77, R.80, H.81, Y.84, V.86, H.90, Y.91, V.94, Y.122, L.125, M.129 20 PLIP interactions: 13 interactions with chain B, 7 interactions with chain A, Hydrophobic interactions: B:L.77, B:L.77, B:Y.84, B:Y.84, B:V.86, B:V.86, B:H.90, B:Y.91, B:V.94, B:Y.122, A:L.41, A:L.41, A:F.42, A:D.55, A:V.56, A:W.59 Hydrogen bonds: B:Y.84 Salt bridges: B:R.80 Metal complexes: B:H.81 Water bridges: A:R.51

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 9 residues within 4Å: Chain A: M.1, I.67, L.71, A.121, A.124, L.125 Chain B: N.63, L.64, I.67 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.71, A:A.124, B:N.63, B:I.67 Hydrogen bonds: A:L.125 Water bridges: A:M.1, A:M.1 MPD.3: 5 residues within 4Å: Chain A: L.26, R.29, R.30, D.33 Chain B: W.100 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.26, A:R.29, B:W.100 Hydrogen bonds: A:R.30 MPD.5: 9 residues within 4Å: Chain A: N.63, L.64, I.67 Chain B: M.1, I.67, L.71, A.121, A.124, L.125 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.71, B:A.124, A:N.63, A:I.67 Hydrogen bonds: B:L.125 Water bridges: B:M.1, B:M.1 MPD.6: 5 residues within 4Å: Chain A: W.100 Chain B: L.26, R.29, R.30, D.33 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.100, B:L.26, B:R.29 Hydrogen bonds: B:R.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teh, A.H. et al., Open and Lys-His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites. Sci Rep (2015)

Release Date

2014-08-06

Peptides

Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hemoglobin-like flavoprotein fused to Roadblock/LC7 domain

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