SMTL ID : 3qqq.1

Crystal structure of non-symbiotic plant hemoglobin from Trema tomentosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: L.56, F.57, S.58, Y.59, H.76, T.79, V.80, M.83, L.107, I.110, H.111, N.114, V.116, H.120, F.121, T.124, Y.152, L.155, I.159 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:L.56, A:L.56, A:F.57, A:F.57, A:F.57, A:Y.59, A:V.80, A:L.107, A:I.110, A:I.110, A:N.114, A:V.116, A:V.116, A:H.120, A:F.121, A:F.121, A:Y.152, A:I.159 Hydrogen bonds: A:N.114 Water bridges: A:N.114 Salt bridges: A:K.72 Metal complexes: A:H.76, A:H.111 HEM.3: 20 residues within 4Å: Chain B: L.56, F.57, Y.59, H.76, T.79, V.80, M.83, R.106, L.107, I.110, H.111, N.114, V.116, H.120, F.121, T.124, Y.152, L.155, V.156, I.159 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:L.56, B:L.56, B:F.57, B:F.57, B:F.57, B:Y.59, B:T.79, B:V.80, B:L.107, B:I.110, B:N.114, B:V.116, B:V.116, B:H.120, B:F.121, B:F.121, B:Y.152, B:V.156, B:I.159 Salt bridges: B:R.106 Metal complexes: B:H.76, B:H.111

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

SO4.2: 2 residues within 4Å: Chain A: W.140, K.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.140 Salt bridges: A:K.133, A:K.145 SO4.4: 3 residues within 4Å: Chain B: K.133, W.140, K.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.140 Salt bridges: B:K.133, B:K.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kakar, S. et al., Crystal structures of Parasponia and Trema hemoglobins: differential heme coordination is linked to quaternary structure. Biochemistry (2011)

Release Date

2011-04-27

Peptides

Non-symbiotic hemoglobin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Non-symbiotic hemoglobin