SMTL ID : 2d2n.2 (1 other biounit)

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: S.42, L.45, F.46, G.48, V.49, H.62, V.66, A.69, L.90, Q.93, H.94, R.97, L.99, N.103, F.104, M.107, Y.131, I.138 Chain D: H.91, Q.95 Ligands: OXY.2, HEM.10 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain D, Hydrophobic interactions: A:L.45, A:F.46, A:F.46, A:V.66, A:A.69, A:L.90, A:R.97, A:L.99, A:N.103, A:F.104, A:M.107, A:Y.131 Hydrogen bonds: A:G.48, A:Q.93, D:Q.95 Salt bridges: A:R.97, D:H.91 Metal complexes: A:H.94 HEM.4: 21 residues within 4Å: Chain B: L.45, F.46, R.48, V.49, H.62, R.65, V.66, L.70, L.90, Q.93, H.94, R.97, I.99, G.103, Y.104, F.107, I.140 Chain C: H.93, Q.97 Ligands: OXY.5, MMC.6 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:V.66, B:L.70, B:L.90, B:R.97, B:I.99, B:Y.104, B:Y.104, B:F.107, B:F.107, B:F.107, B:I.140 Salt bridges: B:R.48, B:H.62, B:R.65, B:R.97, C:H.93 Metal complexes: B:H.94 Hydrogen bonds: C:Q.97 HEM.7: 20 residues within 4Å: Chain B: R.89, Q.93 Chain C: L.49, F.50, G.52, V.53, H.66, R.69, V.70, L.94, Q.97, H.98, R.101, V.104, H.108, F.109, M.112, F.136, I.143 Ligands: OXY.8 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain B, Hydrophobic interactions: C:L.49, C:F.50, C:F.50, C:R.69, C:V.70, C:L.94, C:L.94, C:R.101, C:V.104, C:H.108, C:F.109, C:F.109, C:F.109, C:F.109, C:M.112, C:F.136, C:I.143 Hydrogen bonds: C:G.52, B:Q.93 Salt bridges: C:R.101, C:R.101, B:R.89, B:R.89 Metal complexes: C:H.98 HEM.10: 22 residues within 4Å: Chain A: H.89, Q.93 Chain D: F.39, V.45, M.49, F.50, P.51, Q.64, R.67, V.68, G.71, A.72, Q.95, H.96, I.99, A.106, V.107, L.110, S.111, I.141 Ligands: HEM.1, OXY.11 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain A, Hydrophobic interactions: D:V.45, D:F.50, D:F.50, D:P.51, D:V.68, D:A.72, D:I.99, D:V.107, D:L.110, D:I.141 Hydrogen bonds: D:Q.95, A:Q.93 Salt bridges: D:R.67, A:H.89, A:H.89 Metal complexes: D:H.96

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 7 residues within 4Å: Chain A: F.32, F.46, H.62, V.66, H.94, M.107 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) OXY.5: 6 residues within 4Å: Chain B: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) OXY.8: 5 residues within 4Å: Chain C: F.50, H.66, V.70, H.98 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.66 OXY.11: 5 residues within 4Å: Chain D: F.50, Q.64, V.68, H.96 Ligands: HEM.10 No protein-ligand interaction detected (PLIP)

4 x MMC: METHYL MERCURY ION(Non-covalent)

MMC.3: 7 residues within 4Å: Chain A: F.32, F.46, V.49, V.51, F.59, H.62, C.63 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.63 MMC.6: 8 residues within 4Å: Chain B: G.69, L.70, M.72, C.73, L.90, I.136, I.140 Ligands: HEM.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.73 MMC.9: 5 residues within 4Å: Chain C: F.36, F.50, F.63, H.66, C.67 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.67 MMC.12: 5 residues within 4Å: Chain D: C.3, L.79, R.82, C.85, Y.136 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:C.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Numoto, N. et al., Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi. Proc.Natl.Acad.Sci.USA (2005)

Release Date

2005-10-25

Peptides

Giant hemoglobin, A1(b) globin chain: A
Giant hemoglobin, A2(a5) globin chain: B
Giant hemoglobin, B2(c) globin chain: C
Giant hemoglobin, B1(d) globin chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Giant hemoglobin, A1(b) globin chain

Giant hemoglobin, A2(a5) globin chain

Giant hemoglobin, B2(c) globin chain

Giant hemoglobin, B1(d) globin chain

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