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

Lumbricus Erythrocruorin at 3.5A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-3-3-3-3-1-1-1-mer

Ligands

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

CMO.1: 6 residues within 4Å: Chain A: F.39, F.53, H.69, V.73, H.101 Ligands: HEM.2 No protein-ligand interaction detected (PLIP) CMO.3: 6 residues within 4Å: Chain B: W.34, F.48, H.64, V.68, H.96 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CMO.5: 5 residues within 4Å: Chain C: F.54, H.70, I.74, H.102 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) CMO.7: 6 residues within 4Å: Chain D: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.8 No protein-ligand interaction detected (PLIP) CMO.9: 6 residues within 4Å: Chain E: F.39, F.53, H.69, V.73, H.101 Ligands: HEM.10 No protein-ligand interaction detected (PLIP) CMO.11: 6 residues within 4Å: Chain F: W.34, F.48, H.64, V.68, H.96 Ligands: HEM.12 No protein-ligand interaction detected (PLIP) CMO.13: 5 residues within 4Å: Chain G: F.54, H.70, I.74, H.102 Ligands: HEM.14 No protein-ligand interaction detected (PLIP) CMO.15: 6 residues within 4Å: Chain H: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.16 No protein-ligand interaction detected (PLIP) CMO.17: 6 residues within 4Å: Chain I: F.39, F.53, H.69, V.73, H.101 Ligands: HEM.18 No protein-ligand interaction detected (PLIP) CMO.19: 6 residues within 4Å: Chain J: W.34, F.48, H.64, V.68, H.96 Ligands: HEM.20 No protein-ligand interaction detected (PLIP) CMO.21: 5 residues within 4Å: Chain K: F.54, H.70, I.74, H.102 Ligands: HEM.22 No protein-ligand interaction detected (PLIP) CMO.23: 6 residues within 4Å: Chain L: W.32, F.46, H.62, V.66, H.94 Ligands: HEM.24 No protein-ligand interaction detected (PLIP)

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

HEM.2: 17 residues within 4Å: Chain A: S.49, L.52, F.53, R.55, V.56, H.69, R.72, V.73, H.101, R.104, Y.111, F.112, I.115, F.139 Chain D: H.89, Q.93 Ligands: CMO.1 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain D, Hydrophobic interactions: A:L.52, A:F.53, A:Y.111, A:F.112, A:F.112, A:F.112, A:F.112, A:I.115, A:F.139 Hydrogen bonds: A:R.72, A:R.104, D:Q.93 Salt bridges: A:R.55, A:R.72, A:R.104, D:H.89 pi-Cation interactions: A:H.101 Metal complexes: A:H.101 HEM.4: 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.3 25 PLIP interactions: 22 interactions with chain B, 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.47, B:L.47, B:F.48, B:F.48, B:V.68, B:L.92, B:L.92, B:I.101, B:I.101, B:Y.105, B:F.106, B:F.106, B:F.109, B:E.138, B:I.141 Hydrogen bonds: B:R.67, C:Q.101 Salt bridges: B:R.50, B:H.64, B:R.67, B:R.99, C:H.97 pi-Stacking: B:H.96 Metal complexes: B:H.96, CMO.3 HEM.6: 21 residues within 4Å: Chain B: H.91 Chain C: L.43, L.53, F.54, R.56, V.57, H.70, R.73, I.74, G.77, L.78, Q.101, H.102, R.105, V.108, H.112, F.113, F.116, L.144, I.147 Ligands: CMO.5 16 PLIP interactions: 1 interactions with chain B, 15 interactions with chain C, Salt bridges: B:H.91, C:R.56, C:R.105 Hydrophobic interactions: C:L.43, C:L.53, C:L.53, C:F.54, C:I.74, C:H.112, C:F.113, C:F.113, C:F.113, C:F.116, C:F.116, C:L.144 Metal complexes: C:H.102 HEM.8: 20 residues within 4Å: Chain A: H.96, Q.100 Chain D: I.42, 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 Ligands: CMO.7 19 PLIP interactions: 2 interactions with chain A, 16 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: A:Q.100 Salt bridges: A:H.96, D:R.48, D:R.65, D:R.97 Hydrophobic interactions: D:I.42, D:P.45, D:F.46, D:F.46, D:L.90, D:L.99, D:F.103, D:F.103, D:F.104, D:F.107, D:F.107 pi-Stacking: D:H.62 Metal complexes: D:H.94, CMO.7 HEM.10: 17 residues within 4Å: Chain E: S.49, L.52, F.53, R.55, V.56, H.69, R.72, V.73, H.101, R.104, Y.111, F.112, I.115, F.139 Chain H: H.89, Q.93 Ligands: CMO.9 18 PLIP interactions: 16 interactions with chain E, 2 interactions with chain H, Hydrophobic interactions: E:L.52, E:F.53, E:Y.111, E:F.112, E:F.112, E:F.112, E:F.112, E:I.115, E:F.139 Hydrogen bonds: E:R.72, E:R.104, H:Q.93 Salt bridges: E:R.55, E:R.72, E:R.104, H:H.89 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.11 23 PLIP interactions: 20 interactions with chain F, 2 interactions with chain G, 1 Ligand-Ligand interactions Hydrophobic interactions: F:L.47, F:L.47, F:F.48, F:F.48, F:V.68, F:L.92, F:L.92, F:I.101, F:Y.105, F:F.106, F:F.106, F:F.109, F:E.138, F:I.141 Hydrogen bonds: F:R.67, G:Q.101 Salt bridges: F:R.50, F:H.64, F:R.67, F:R.99, G:H.97 Metal complexes: F:H.96, CMO.11 HEM.14: 22 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, Q.101, H.102, R.105, V.108, H.112, F.113, F.116, L.144, I.147 Ligands: CMO.13 18 PLIP interactions: 16 interactions with chain G, 2 interactions with chain F, Hydrophobic interactions: G:L.43, G:L.53, G:L.53, G:F.54, G:I.74, G:H.112, G:F.113, G:F.113, G:F.113, G:F.116, G:F.116, G:L.144 Salt bridges: G:R.56, G:H.70, G:R.105, F:H.91 Metal complexes: G:H.102 Hydrogen bonds: F:Q.95 HEM.16: 19 residues within 4Å: Chain E: H.96, Q.100 Chain H: I.42, P.45, F.46, R.48, V.49, H.62, V.66, L.70, L.90, Q.93, H.94, R.97, L.99, F.103, F.104, F.107 Ligands: CMO.15 19 PLIP interactions: 2 interactions with chain E, 17 interactions with chain H, Hydrogen bonds: E:Q.100 Salt bridges: E:H.96, H:R.48, H:R.65, H:R.97 Hydrophobic interactions: H:I.42, H:P.45, H:F.46, H:F.46, H:L.90, H:L.99, H:F.103, H:F.104, H:F.107, H:F.107 pi-Stacking: H:H.62, H:H.62, H:H.94 Metal complexes: H:H.94 HEM.18: 17 residues within 4Å: Chain I: S.49, L.52, F.53, R.55, V.56, H.69, R.72, V.73, H.101, R.104, Y.111, F.112, I.115, F.139 Chain L: H.89, Q.93 Ligands: CMO.17 19 PLIP interactions: 17 interactions with chain I, 2 interactions with chain L, Hydrophobic interactions: I:L.52, I:F.53, I:Y.111, I:F.112, I:F.112, I:F.112, I:F.112, I:I.115, I:F.139 Hydrogen bonds: I:R.72, I:R.104, L:Q.93 Salt bridges: I:R.55, I:H.69, I:R.72, I:R.104, L:H.89 pi-Cation interactions: I:H.101 Metal complexes: I:H.101 HEM.20: 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.19 23 PLIP interactions: 20 interactions with chain J, 2 interactions with chain K, 1 Ligand-Ligand interactions Hydrophobic interactions: J:L.47, J:L.47, J:F.48, J:F.48, J:V.68, J:L.92, J:L.92, J:I.101, J:Y.105, J:F.106, J:F.106, J:F.109, J:E.138, J:I.141 Hydrogen bonds: J:R.67, K:Q.101 Salt bridges: J:R.50, J:H.64, J:R.67, J:R.99, K:H.97 Metal complexes: J:H.96, CMO.19 HEM.22: 21 residues within 4Å: Chain J: H.91 Chain K: L.43, L.53, F.54, R.56, V.57, H.70, R.73, I.74, G.77, L.78, Q.101, H.102, R.105, V.108, H.112, F.113, F.116, L.144, I.147 Ligands: CMO.21 17 PLIP interactions: 15 interactions with chain K, 1 interactions with chain J, 1 Ligand-Ligand interactions Hydrophobic interactions: K:L.43, K:L.53, K:L.53, K:F.54, K:I.74, K:H.112, K:F.113, K:F.113, K:F.113, K:F.116, K:F.116, K:L.144 Salt bridges: K:R.56, K:R.105, J:H.91 Metal complexes: K:H.102, CMO.21 HEM.24: 19 residues within 4Å: Chain I: H.96, Q.100 Chain L: I.42, P.45, F.46, R.48, V.49, H.62, V.66, L.70, L.90, Q.93, H.94, R.97, L.99, F.103, F.104, F.107 Ligands: CMO.23 18 PLIP interactions: 16 interactions with chain L, 2 interactions with chain I, Hydrophobic interactions: L:I.42, L:P.45, L:F.46, L:F.46, L:L.90, L:L.99, L:F.103, L:F.103, L:F.104, L:F.107, L:F.107 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

4 x CA: CALCIUM ION(Non-covalent)

CA.25: 6 residues within 4Å: Chain M: L.73, D.76, E.78, D.80, D.86, E.87 5 PLIP interactions: 5 interactions with chain M Metal complexes: M:L.73, M:D.76, M:E.78, M:D.80, M:D.86 CA.26: 4 residues within 4Å: Chain G: E.9, D.86 Chain M: W.109, D.114 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.9, G:E.9, G:D.86 CA.28: 6 residues within 4Å: Chain N: L.72, D.75, H.77, D.79, D.85, E.86 5 PLIP interactions: 5 interactions with chain N Metal complexes: N:L.72, N:D.75, N:H.77, N:D.79, N:D.85 CA.29: 6 residues within 4Å: Chain O: F.74, D.77, H.79, D.81, D.87, E.88 5 PLIP interactions: 5 interactions with chain O Metal complexes: O:F.74, O:D.77, O:H.79, O:D.81, O:D.87

1 x ZN: ZINC ION(Non-covalent)

ZN.27: 5 residues within 4Å: Chain N: R.114, S.144, S.155, H.181, R.200 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Royer Jr., W.E. et al., Lumbricus erythrocruorin at 3.5 a resolution: architecture of a megadalton respiratory complex. Structure (2006)

Release Date

2006-07-18

Peptides

Extracellular globin 4: AEI
Extracellular globin 2: BFJ
Extracellular globin-3: CGK
Hemoglobin chain d1: DHL
Hemoglobin linker chain L1: M
Extracellular hemoglobin linker L2 subunit: N
Extracellular hemoglobin linker L3 subunit: O

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

M
M

N
N

O
O

Extracellular globin 4

Extracellular globin 2

Extracellular globin-3

Hemoglobin chain d1

Hemoglobin linker chain L1

Extracellular hemoglobin linker L2 subunit

Extracellular hemoglobin linker L3 subunit

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