SMTL ID : 1x9f.1

Hemoglobin Dodecamer from Lumbricus Erythrocruorin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: L.42, L.52, F.53, R.55, V.56, H.69, R.72, G.76, L.77, L.97, Q.100, H.101, R.104, V.107, Y.111, F.112, I.115, F.139 Chain D: H.89, Q.93 Ligands: CMO.2 26 PLIP interactions: 2 interactions with chain D, 24 interactions with chain A, Hydrogen bonds: D:Q.93, A:Q.100 Salt bridges: D:H.89, A:R.55, A:R.72, A:R.104 Hydrophobic interactions: A:L.42, A:L.52, A:L.52, A:F.53, A:V.56, A:L.97, A:L.97, A:V.107, A:V.107, A:Y.111, A:F.112, A:F.112, A:I.115, A:F.139 Water bridges: A:V.56 pi-Stacking: A:H.69, A:H.101, A:H.101 pi-Cation interactions: A:H.101 Metal complexes: A:H.101 HEM.3: 20 residues within 4Å: Chain B: L.47, F.48, R.50, H.64, R.67, V.68, L.72, L.92, Q.95, H.96, R.99, I.101, Y.105, F.106, F.109, E.138, I.141 Chain C: H.97, Q.101 Ligands: CMO.4 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:L.47, B:F.48, B:F.48, B:I.101, B:Y.105, B:F.106, B:F.106, B:F.109, B:F.109, B:E.138, B:I.141 Water bridges: B:V.51 Salt bridges: B:R.50, B:R.67, B:R.99, C:H.97 pi-Stacking: B:W.34, B:H.64 Metal complexes: B:H.96 Hydrogen bonds: C:Q.101 HEM.6: 22 residues within 4Å: Chain B: H.91, Q.95 Chain C: L.43, L.53, F.54, R.56, V.57, H.70, R.73, I.74, G.77, L.78, L.98, Q.101, H.102, R.105, V.108, H.112, F.113, F.116, L.144 Ligands: CMO.7 24 PLIP interactions: 22 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:L.43, C:L.53, C:L.53, C:F.54, C:F.54, C:I.74, C:V.108, C:V.108, C:H.112, C:F.113, C:F.113, C:F.113, C:F.116, C:F.116, C:L.144 Hydrogen bonds: C:Q.101, B:Q.95 Water bridges: C:H.70, C:R.73 Salt bridges: C:R.56, C:R.105, B:H.91 pi-Stacking: C:H.70 Metal complexes: C:H.102 HEM.8: 20 residues within 4Å: Chain A: H.96, Q.100 Chain D: P.45, F.46, R.48, V.49, H.62, R.65, V.66, L.70, L.90, Q.93, H.94, R.97, L.99, F.103, F.104, F.107, I.136 Ligands: CMO.9 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain A, Hydrophobic interactions: D:P.45, D:P.45, D:F.46, D:V.49, D:V.66, D:L.90, D:L.99, D:L.99, D:F.103, D:F.103, D:F.104, D:F.107, D:F.107, D:I.136 Salt bridges: D:R.48, D:R.65, D:R.97, A:H.96 pi-Stacking: D:H.62 Metal complexes: D:H.94 Hydrogen bonds: A:Q.100 HEM.10: 21 residues within 4Å: Chain E: L.42, L.52, F.53, R.55, V.56, H.69, R.72, G.76, L.77, L.97, Q.100, H.101, R.104, V.107, Y.111, F.112, I.115, F.139 Chain H: H.89, Q.93 Ligands: CMO.11 20 PLIP interactions: 2 interactions with chain H, 18 interactions with chain E, Hydrogen bonds: H:Q.93 Salt bridges: H:H.89, E:R.55, E:R.104 Hydrophobic interactions: E:L.42, E:L.52, E:V.56, E:L.97, E:V.107, E:Y.111, E:F.112, E:F.112, E:I.115, E:F.139 Water bridges: E:H.69 pi-Stacking: E:H.69, E:H.101, E:H.101 pi-Cation interactions: E:H.101 Metal complexes: E:H.101 HEM.12: 20 residues within 4Å: Chain F: L.47, F.48, R.50, H.64, R.67, V.68, L.72, L.92, Q.95, H.96, R.99, I.101, Y.105, F.106, F.109, E.138, I.141 Chain G: H.97, Q.101 Ligands: CMO.13 23 PLIP interactions: 21 interactions with chain F, 2 interactions with chain G, Hydrophobic interactions: F:L.47, F:F.48, F:F.48, F:L.92, F:I.101, F:Y.105, F:F.106, F:F.106, F:F.109, F:F.109, F:E.138, F:I.141 Hydrogen bonds: F:Q.95, G:Q.101 Water bridges: F:L.47, F:R.67, F:R.99 Salt bridges: F:R.50, F:R.67, F:R.99, G:H.97 pi-Stacking: F:H.64 Metal complexes: F:H.96 HEM.15: 23 residues within 4Å: Chain F: H.91, Q.95 Chain G: L.43, L.53, F.54, R.56, V.57, H.70, R.73, I.74, G.77, L.78, L.98, Q.101, H.102, R.105, V.108, H.112, F.113, F.116, L.144, I.147 Ligands: CMO.16 23 PLIP interactions: 2 interactions with chain F, 21 interactions with chain G, Hydrogen bonds: F:Q.95, G:Q.101 Salt bridges: F:H.91, G:R.56, G:R.105 Hydrophobic interactions: G:L.43, G:L.53, G:F.54, G:F.54, G:I.74, G:V.108, G:H.112, G:F.113, G:F.113, G:F.113, G:F.116, G:F.116, G:L.144, G:I.147 Water bridges: G:H.70, G:R.73 pi-Stacking: G:H.70 Metal complexes: G:H.102 HEM.17: 21 residues within 4Å: Chain E: H.96, Q.100 Chain H: P.45, F.46, R.48, V.49, H.62, R.65, V.66, G.69, L.70, L.90, Q.93, H.94, R.97, L.99, F.103, F.104, F.107, I.136 Ligands: CMO.18 19 PLIP interactions: 2 interactions with chain E, 17 interactions with chain H, Hydrogen bonds: E:Q.100, H:Q.93 Salt bridges: E:H.96, H:R.48, H:R.97 Hydrophobic interactions: H:P.45, H:P.45, H:F.46, H:V.49, H:L.99, H:L.99, H:F.103, H:F.103, H:F.104, H:F.107, H:F.107, H:I.136 pi-Stacking: H:H.62 Metal complexes: H:H.94 HEM.19: 21 residues within 4Å: Chain I: L.42, L.52, F.53, R.55, V.56, H.69, R.72, G.76, L.77, L.97, Q.100, H.101, R.104, V.107, Y.111, F.112, I.115, F.139 Chain L: H.89, Q.93 Ligands: CMO.20 27 PLIP interactions: 25 interactions with chain I, 2 interactions with chain L, Hydrophobic interactions: I:L.42, I:L.52, I:L.52, I:F.53, I:V.56, I:L.97, I:R.104, I:V.107, I:V.107, I:Y.111, I:F.112, I:F.112, I:F.112, I:F.112, I:I.115, I:F.139 Hydrogen bonds: I:Q.100, L:Q.93 Salt bridges: I:R.55, I:R.104, L:H.89 pi-Stacking: I:H.69, I:H.69, I:H.101, I:H.101 pi-Cation interactions: I:H.101 Metal complexes: I:H.101 HEM.21: 20 residues within 4Å: Chain J: L.47, F.48, R.50, H.64, R.67, V.68, L.72, L.92, Q.95, H.96, R.99, I.101, Y.105, F.106, F.109, E.138, I.141 Chain K: H.97, Q.101 Ligands: CMO.22 21 PLIP interactions: 19 interactions with chain J, 2 interactions with chain K, Hydrophobic interactions: J:F.48, J:F.48, J:L.92, J:L.92, J:I.101, J:I.101, J:Y.105, J:F.106, J:F.106, J:F.109, J:F.109, J:E.138, J:I.141 Hydrogen bonds: J:Q.95, K:Q.101 Salt bridges: J:R.50, J:R.67, J:R.99, K:H.97 pi-Stacking: J:H.64 Metal complexes: J:H.96 HEM.24: 22 residues within 4Å: Chain J: H.91, Q.95 Chain K: L.43, L.53, F.54, R.56, V.57, H.70, R.73, I.74, G.77, L.78, L.98, Q.101, H.102, R.105, V.108, H.112, F.113, F.116, L.144 Ligands: CMO.25 23 PLIP interactions: 21 interactions with chain K, 2 interactions with chain J, Hydrophobic interactions: K:L.53, K:L.53, K:F.54, K:F.54, K:V.57, K:I.74, K:V.108, K:V.108, K:H.112, K:F.113, K:F.113, K:F.113, K:F.116, K:F.116, K:L.144 Hydrogen bonds: K:Q.101, J:Q.95 Water bridges: K:R.105 Salt bridges: K:R.56, K:R.105, J:H.91 pi-Stacking: K:H.70 Metal complexes: K:H.102 HEM.26: 20 residues within 4Å: Chain I: H.96, Q.100 Chain L: P.45, F.46, R.48, V.49, H.62, R.65, V.66, L.70, L.90, Q.93, H.94, R.97, L.99, F.103, F.104, F.107, I.136 Ligands: CMO.27 21 PLIP interactions: 19 interactions with chain L, 2 interactions with chain I, Hydrophobic interactions: L:P.45, L:P.45, L:F.46, L:V.49, L:V.66, L:L.99, L:L.99, L:F.103, L:F.103, L:F.104, L:F.107, L:F.107, L:I.136 Water bridges: L:R.65 Salt bridges: L:R.48, L:R.65, L:R.97, I:H.96 pi-Stacking: L:H.62 Metal complexes: L:H.94 Hydrogen bonds: I:Q.100

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

CMO.2: 5 residues within 4Å: Chain A: F.39, F.53, H.69, V.73 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.69 CMO.4: 5 residues within 4Å: Chain B: W.34, F.48, H.64, V.68 Ligands: HEM.3 No protein-ligand interaction detected (PLIP) CMO.7: 5 residues within 4Å: Chain C: L.40, F.54, H.70, I.74 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) CMO.9: 5 residues within 4Å: Chain D: W.32, F.46, H.62, V.66 Ligands: HEM.8 No protein-ligand interaction detected (PLIP) CMO.11: 5 residues within 4Å: Chain E: F.39, F.53, H.69, V.73 Ligands: HEM.10 No protein-ligand interaction detected (PLIP) CMO.13: 5 residues within 4Å: Chain F: W.34, F.48, H.64, V.68 Ligands: HEM.12 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.64 CMO.16: 5 residues within 4Å: Chain G: L.40, F.54, H.70, I.74 Ligands: HEM.15 No protein-ligand interaction detected (PLIP) CMO.18: 5 residues within 4Å: Chain H: W.32, F.46, H.62, V.66 Ligands: HEM.17 No protein-ligand interaction detected (PLIP) CMO.20: 5 residues within 4Å: Chain I: F.39, F.53, H.69, V.73 Ligands: HEM.19 No protein-ligand interaction detected (PLIP) CMO.22: 5 residues within 4Å: Chain J: W.34, F.48, H.64, V.68 Ligands: HEM.21 No protein-ligand interaction detected (PLIP) CMO.25: 5 residues within 4Å: Chain K: L.40, F.54, H.70, I.74 Ligands: HEM.24 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:H.70 CMO.27: 5 residues within 4Å: Chain L: W.32, F.46, H.62, V.66 Ligands: HEM.26 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:H.62

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 4 residues within 4Å: Chain B: R.50 Chain C: D.96, H.97, H.100 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Salt bridges: C:H.97, C:H.100, B:R.50 PO4.14: 4 residues within 4Å: Chain F: R.50 Chain G: D.96, H.97, H.100 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G Salt bridges: F:R.50, G:H.97, G:H.100 PO4.23: 4 residues within 4Å: Chain J: R.50 Chain K: D.96, H.97, H.100 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:H.97 Salt bridges: K:H.97, K:H.100, J:R.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strand, K. et al., Crystal structure of the hemoglobin dodecamer from lumbricus erythrocruorin: allosteric core of giant annelid respiratory complexes. J.Mol.Biol. (2004)

Release Date

2004-11-30

Peptides

Globin IV, extracellular: AEI
Globin II, extracellular: BFJ
Globin III, extracellular: CGK
hemoglobin chain d1: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

Globin IV, extracellular

Globin II, extracellular

Globin III, extracellular

hemoglobin chain d1

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