SMTL ID : 5m3l.1

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris hemoglobin

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

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

Ligands

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

HEM.1: 10 residues within 4Å: Chain A: L.52, F.53, H.69, L.97, H.101, R.104, F.112, I.115 Chain D: H.89 Ligands: HEM.4 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: A:L.52, A:F.53, A:F.53, A:L.97, A:F.112, A:I.115 pi-Stacking: A:H.69 Salt bridges: A:R.104, D:H.89 Metal complexes: A:H.101 HEM.2: 14 residues within 4Å: Chain C: H.97 Chain B: L.47, F.48, H.64, R.67, L.72, L.92, Q.95, H.96, R.99, Y.105, F.106, F.109, E.138 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain B, Hydrophobic interactions: B:F.48, B:L.72, B:L.92, B:Y.105, B:F.106, B:F.109 Salt bridges: C:H.97, B:R.67, B:R.99 Metal complexes: B:H.96 HEM.3: 15 residues within 4Å: Chain C: L.43, R.56, V.57, H.70, R.73, I.74, L.78, L.98, Q.101, H.102, R.105, H.112, F.113, F.116 Chain B: H.91 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:L.43, C:I.74, C:L.98, C:Q.101, C:H.112, C:F.113, C:F.116, C:F.116 pi-Stacking: C:H.102 Salt bridges: C:R.56, C:R.73, C:R.105, B:H.91 Metal complexes: C:H.102 HEM.4: 12 residues within 4Å: Chain A: H.96 Chain D: F.46, V.49, H.62, R.65, L.70, L.90, H.94, R.97, F.104, F.107 Ligands: HEM.1 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain D, Hydrophobic interactions: D:F.46, D:F.46, D:L.70, D:L.90, D:L.90, D:F.104, D:F.107 Hydrogen bonds: D:R.65 Salt bridges: A:H.96, D:R.48, D:R.97 Metal complexes: D:H.94 pi-Stacking: D:H.62 HEM.5: 11 residues within 4Å: Chain H: H.89 Chain E: L.52, F.53, R.55, H.69, L.97, H.101, R.104, F.112, I.115 Ligands: HEM.8 10 PLIP interactions: 1 interactions with chain H, 9 interactions with chain E, Hydrophobic interactions: E:L.52, E:F.53, E:F.53, E:L.97, E:F.112, E:I.115 Salt bridges: H:H.89, E:R.55, E:R.104 Metal complexes: E:H.101 HEM.6: 14 residues within 4Å: Chain G: H.97, Q.101 Chain F: L.47, F.48, H.64, R.67, L.72, L.92, Q.95, H.96, R.99, Y.105, F.106, F.109 14 PLIP interactions: 2 interactions with chain G, 12 interactions with chain F Hydrogen bonds: G:Q.101, F:Q.95 Hydrophobic interactions: F:F.48, F:F.48, F:L.72, F:L.92, F:Y.105, F:F.106, F:F.109 Salt bridges: G:H.97, F:R.67, F:R.99 Metal complexes: F:H.96 pi-Stacking: F:H.64 HEM.7: 15 residues within 4Å: Chain G: L.43, F.54, V.57, H.70, R.73, I.74, L.78, L.98, Q.101, H.102, R.105, H.112, F.113, F.116 Chain F: H.91 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:L.43, G:F.54, G:I.74, G:I.74, G:L.98, G:L.98, G:Q.101, G:H.112, G:F.113, G:F.116, G:F.116 pi-Stacking: G:H.102 Salt bridges: G:R.73, G:R.105, F:H.91 Metal complexes: G:H.102 HEM.8: 11 residues within 4Å: Chain H: F.46, R.48, H.62, R.65, Q.93, H.94, R.97, F.104, F.107 Chain E: H.96 Ligands: HEM.5 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain E, Hydrophobic interactions: H:F.46, H:F.46, H:Q.93, H:F.104, H:F.107 pi-Stacking: H:H.62, H:H.94 Salt bridges: H:R.65, H:R.97, E:H.96 Metal complexes: H:H.94 HEM.9: 13 residues within 4Å: Chain I: L.52, F.53, R.55, H.69, L.97, Q.100, H.101, R.104, Y.111, F.112, I.115 Chain L: H.89 Ligands: HEM.12 12 PLIP interactions: 11 interactions with chain I, 1 interactions with chain L, Hydrophobic interactions: I:L.52, I:F.53, I:F.53, I:L.97, I:Y.111, I:F.112, I:I.115 Hydrogen bonds: I:Q.100 Salt bridges: I:R.55, I:R.104, L:H.89 Metal complexes: I:H.101 HEM.10: 15 residues within 4Å: Chain K: H.97, Q.101 Chain J: S.44, L.47, F.48, H.64, R.67, L.72, L.92, Q.95, H.96, R.99, Y.105, F.106, F.109 13 PLIP interactions: 2 interactions with chain K, 11 interactions with chain J, Hydrogen bonds: K:Q.101, J:Q.95 Hydrophobic interactions: J:F.48, J:L.72, J:L.92, J:Y.105, J:F.106, J:F.109 Salt bridges: K:H.97, J:R.67, J:R.99 Metal complexes: J:H.96 pi-Stacking: J:H.64 HEM.11: 15 residues within 4Å: Chain K: L.43, F.54, V.57, H.70, R.73, I.74, L.78, L.98, Q.101, H.102, R.105, H.112, F.113, F.116 Chain J: H.91 16 PLIP interactions: 15 interactions with chain K, 1 interactions with chain J, Hydrophobic interactions: K:L.43, K:F.54, K:I.74, K:L.98, K:Q.101, K:H.112, K:F.113, K:F.116, K:F.116 pi-Stacking: K:H.102 Salt bridges: K:R.56, K:H.70, K:R.73, K:R.105, J:H.91 Metal complexes: K:H.102 HEM.12: 10 residues within 4Å: Chain I: H.96 Chain L: F.46, R.48, H.62, R.65, L.70, L.90, H.94, F.107 Ligands: HEM.9 10 PLIP interactions: 1 interactions with chain I, 9 interactions with chain L, Hydrophobic interactions: L:F.46, L:F.46, L:L.90, L:F.107, L:F.107 Hydrogen bonds: L:R.65 Salt bridges: I:H.96, L:R.48 Metal complexes: L:H.94 pi-Stacking: L:H.62

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Afanasyev, P. et al., Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin. IUCrJ (2017)

Release Date

2017-09-13

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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